I: pbuilder: network access will be disabled during build I: Current time: Sat Sep 21 06:55:28 -12 2024 I: pbuilder-time-stamp: 1726944928 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: using eatmydata during job I: Copying source file I: copying [pyranges_0.0.111+ds-8.dsc] I: copying [./pyranges_0.0.111+ds.orig.tar.xz] I: copying [./pyranges_0.0.111+ds-8.debian.tar.xz] I: Extracting source gpgv: Signature made Sat Sep 21 11:53:08 2024 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./pyranges_0.0.111+ds-8.dsc: no acceptable signature found dpkg-source: info: extracting pyranges in pyranges-0.0.111+ds dpkg-source: info: unpacking pyranges_0.0.111+ds.orig.tar.xz dpkg-source: info: unpacking pyranges_0.0.111+ds-8.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix_dtype.patch dpkg-source: info: applying reorder.patch dpkg-source: info: applying numpy_1.24.patch dpkg-source: info: applying healthcheck-all.patch dpkg-source: info: applying no_install_depends_cython.patch dpkg-source: info: applying pandas2.0.patch dpkg-source: info: applying fix-test_unary.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/9137/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='i386' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=11 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='cf3bccf43eca477890f24bcfc678050d' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' LD_LIBRARY_PATH='/usr/lib/libeatmydata' LD_PRELOAD='libeatmydata.so' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='9137' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.JLukkBmS/pbuilderrc_L12K --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.JLukkBmS/b1 --logfile b1/build.log pyranges_0.0.111+ds-8.dsc' SUDO_GID='112' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://46.16.76.132:3128' I: uname -a Linux ionos2-i386 6.1.0-25-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.106-3 (2024-08-26) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/9137/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: i386 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-sequence-python3, python3-setuptools, python3-all, python3-ncls, python3-pyrle, python3-pytest, python3-pytest-xdist, python3-sorted-nearest, python3-hypothesis, bedtools, samtools dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19774 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-sequence-python3; however: Package dh-sequence-python3 is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-all; however: Package python3-all is not installed. pbuilder-satisfydepends-dummy depends on python3-ncls; however: Package python3-ncls is not installed. pbuilder-satisfydepends-dummy depends on python3-pyrle; however: Package python3-pyrle is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest; however: Package python3-pytest is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest-xdist; however: Package python3-pytest-xdist is not installed. pbuilder-satisfydepends-dummy depends on python3-sorted-nearest; however: Package python3-sorted-nearest is not installed. pbuilder-satisfydepends-dummy depends on python3-hypothesis; however: Package python3-hypothesis is not installed. pbuilder-satisfydepends-dummy depends on bedtools; however: Package bedtools is not installed. pbuilder-satisfydepends-dummy depends on samtools; however: Package samtools is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bedtools{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libblas3{a} libbrotli1{a} libcom-err2{a} libcurl3t64-gnutls{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libgssapi-krb5-2{a} libhts3t64{a} libhtscodecs2{a} libicu72{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} libldap-2.5-0{a} libmagic-mgc{a} libmagic1t64{a} libncurses6{a} libnghttp2-14{a} libnghttp3-9{a} libngtcp2-16{a} libngtcp2-crypto-gnutls8{a} libnsl2{a} libpipeline1{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1t64{a} libtirpc-common{a} libtirpc3t64{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} python3{a} python3-all{a} python3-attr{a} python3-autocommand{a} python3-dateutil{a} python3-execnet{a} python3-hypothesis{a} python3-inflect{a} python3-iniconfig{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-minimal{a} python3-more-itertools{a} python3-natsort{a} python3-ncls{a} python3-numpy{a} python3-packaging{a} python3-pandas{a} python3-pandas-lib{a} python3-pkg-resources{a} python3-pluggy{a} python3-pyrle{a} python3-pytest{a} python3-pytest-xdist{a} python3-setuptools{a} python3-six{a} python3-sorted-nearest{a} python3-sortedcontainers{a} python3-tabulate{a} python3-typeguard{a} python3-typing-extensions{a} python3-tz{a} python3-zipp{a} python3.12{a} python3.12-minimal{a} readline-common{a} samtools{a} sensible-utils{a} tzdata{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl krb5-locales libarchive-cpio-perl libgpm2 libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix python3-bottleneck python3-bs4 python3-click python3-html5lib python3-jinja2 python3-lxml python3-matplotlib python3-numexpr python3-odf python3-openpyxl python3-pygments python3-scipy python3-tables wget 0 packages upgraded, 104 newly installed, 0 to remove and 0 not upgraded. Need to get 48.8 MB of archives. After unpacking 218 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main i386 libpython3.12-minimal i386 3.12.6-1 [813 kB] Get: 2 http://deb.debian.org/debian unstable/main i386 libexpat1 i386 2.6.3-1 [107 kB] Get: 3 http://deb.debian.org/debian unstable/main i386 python3.12-minimal i386 3.12.6-1 [2242 kB] Get: 4 http://deb.debian.org/debian unstable/main i386 python3-minimal i386 3.12.6-1 [26.7 kB] Get: 5 http://deb.debian.org/debian unstable/main i386 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian unstable/main i386 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian unstable/main i386 tzdata all 2024a-4 [255 kB] Get: 8 http://deb.debian.org/debian unstable/main i386 libkrb5support0 i386 1.21.3-3 [34.9 kB] Get: 9 http://deb.debian.org/debian unstable/main i386 libcom-err2 i386 1.47.1-1 [23.1 kB] Get: 10 http://deb.debian.org/debian unstable/main i386 libk5crypto3 i386 1.21.3-3 [83.6 kB] Get: 11 http://deb.debian.org/debian unstable/main i386 libkeyutils1 i386 1.6.3-3 [9432 B] Get: 12 http://deb.debian.org/debian unstable/main i386 libkrb5-3 i386 1.21.3-3 [350 kB] Get: 13 http://deb.debian.org/debian unstable/main i386 libgssapi-krb5-2 i386 1.21.3-3 [146 kB] Get: 14 http://deb.debian.org/debian unstable/main i386 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 15 http://deb.debian.org/debian unstable/main i386 libtirpc3t64 i386 1.3.4+ds-1.3 [90.2 kB] Get: 16 http://deb.debian.org/debian unstable/main i386 libnsl2 i386 1.3.0-3+b2 [42.4 kB] Get: 17 http://deb.debian.org/debian unstable/main i386 readline-common all 8.2-5 [69.3 kB] Get: 18 http://deb.debian.org/debian unstable/main i386 libreadline8t64 i386 8.2-5 [173 kB] Get: 19 http://deb.debian.org/debian unstable/main i386 libpython3.12-stdlib i386 3.12.6-1 [1961 kB] Get: 20 http://deb.debian.org/debian unstable/main i386 python3.12 i386 3.12.6-1 [669 kB] Get: 21 http://deb.debian.org/debian unstable/main i386 libpython3-stdlib i386 3.12.6-1 [9692 B] Get: 22 http://deb.debian.org/debian unstable/main i386 python3 i386 3.12.6-1 [27.8 kB] Get: 23 http://deb.debian.org/debian unstable/main i386 sensible-utils all 0.0.24 [24.8 kB] Get: 24 http://deb.debian.org/debian unstable/main i386 libmagic-mgc i386 1:5.45-3 [314 kB] Get: 25 http://deb.debian.org/debian unstable/main i386 libmagic1t64 i386 1:5.45-3 [114 kB] Get: 26 http://deb.debian.org/debian unstable/main i386 file i386 1:5.45-3 [42.9 kB] Get: 27 http://deb.debian.org/debian unstable/main i386 gettext-base i386 0.22.5-2 [201 kB] Get: 28 http://deb.debian.org/debian unstable/main i386 libuchardet0 i386 0.0.8-1+b1 [69.1 kB] Get: 29 http://deb.debian.org/debian unstable/main i386 groff-base i386 1.23.0-5 [1196 kB] Get: 30 http://deb.debian.org/debian unstable/main i386 bsdextrautils i386 2.40.2-8 [102 kB] Get: 31 http://deb.debian.org/debian unstable/main i386 libpipeline1 i386 1.5.8-1 [41.2 kB] Get: 32 http://deb.debian.org/debian unstable/main i386 man-db i386 2.13.0-1 [1428 kB] Get: 33 http://deb.debian.org/debian unstable/main i386 m4 i386 1.4.19-4 [293 kB] Get: 34 http://deb.debian.org/debian unstable/main i386 autoconf all 2.72-3 [493 kB] Get: 35 http://deb.debian.org/debian unstable/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 36 http://deb.debian.org/debian unstable/main i386 automake all 1:1.16.5-1.3 [823 kB] Get: 37 http://deb.debian.org/debian unstable/main i386 autopoint all 0.22.5-2 [723 kB] Get: 38 http://deb.debian.org/debian unstable/main i386 bedtools i386 2.31.1+dfsg-2 [745 kB] Get: 39 http://deb.debian.org/debian unstable/main i386 libdebhelper-perl all 13.20 [89.7 kB] Get: 40 http://deb.debian.org/debian unstable/main i386 libtool all 2.4.7-7 [517 kB] Get: 41 http://deb.debian.org/debian unstable/main i386 dh-autoreconf all 20 [17.1 kB] Get: 42 http://deb.debian.org/debian unstable/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 43 http://deb.debian.org/debian unstable/main i386 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 44 http://deb.debian.org/debian unstable/main i386 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 45 http://deb.debian.org/debian unstable/main i386 libelf1t64 i386 0.191-2 [194 kB] Get: 46 http://deb.debian.org/debian unstable/main i386 dwz i386 0.15-1+b1 [116 kB] Get: 47 http://deb.debian.org/debian unstable/main i386 libicu72 i386 72.1-5 [9550 kB] Get: 48 http://deb.debian.org/debian unstable/main i386 libxml2 i386 2.12.7+dfsg-3+b1 [704 kB] Get: 49 http://deb.debian.org/debian unstable/main i386 gettext i386 0.22.5-2 [1631 kB] Get: 50 http://deb.debian.org/debian unstable/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 51 http://deb.debian.org/debian unstable/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 52 http://deb.debian.org/debian unstable/main i386 debhelper all 13.20 [915 kB] Get: 53 http://deb.debian.org/debian unstable/main i386 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 54 http://deb.debian.org/debian unstable/main i386 python3-more-itertools all 10.4.0-1 [63.7 kB] Get: 55 http://deb.debian.org/debian unstable/main i386 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 56 http://deb.debian.org/debian unstable/main i386 python3-typeguard all 4.3.0-1 [36.5 kB] Get: 57 http://deb.debian.org/debian unstable/main i386 python3-inflect all 7.3.1-2 [32.4 kB] Get: 58 http://deb.debian.org/debian unstable/main i386 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 59 http://deb.debian.org/debian unstable/main i386 python3-jaraco.functools all 4.0.2-1 [11.7 kB] Get: 60 http://deb.debian.org/debian unstable/main i386 python3-pkg-resources all 74.1.2-2 [213 kB] Get: 61 http://deb.debian.org/debian unstable/main i386 python3-zipp all 3.20.2-1 [10.3 kB] Get: 62 http://deb.debian.org/debian unstable/main i386 python3-setuptools all 74.1.2-2 [736 kB] Get: 63 http://deb.debian.org/debian unstable/main i386 dh-python all 6.20240824 [109 kB] Get: 64 http://deb.debian.org/debian unstable/main i386 libblas3 i386 3.12.0-3 [140 kB] Get: 65 http://deb.debian.org/debian unstable/main i386 libbrotli1 i386 1.1.0-2+b4 [309 kB] Get: 66 http://deb.debian.org/debian unstable/main i386 libsasl2-modules-db i386 2.1.28+dfsg1-8 [20.6 kB] Get: 67 http://deb.debian.org/debian unstable/main i386 libsasl2-2 i386 2.1.28+dfsg1-8 [61.0 kB] Get: 68 http://deb.debian.org/debian unstable/main i386 libldap-2.5-0 i386 2.5.18+dfsg-3 [200 kB] Get: 69 http://deb.debian.org/debian unstable/main i386 libnghttp2-14 i386 1.63.0-1 [82.7 kB] Get: 70 http://deb.debian.org/debian unstable/main i386 libnghttp3-9 i386 1.4.0-1 [74.3 kB] Get: 71 http://deb.debian.org/debian unstable/main i386 libngtcp2-16 i386 1.6.0-1 [154 kB] Get: 72 http://deb.debian.org/debian unstable/main i386 libngtcp2-crypto-gnutls8 i386 1.6.0-1 [20.2 kB] Get: 73 http://deb.debian.org/debian unstable/main i386 libpsl5t64 i386 0.21.2-1.1 [57.4 kB] Get: 74 http://deb.debian.org/debian unstable/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-2+b4 [62.0 kB] Get: 75 http://deb.debian.org/debian unstable/main i386 libssh2-1t64 i386 1.11.0-7 [226 kB] Get: 76 http://deb.debian.org/debian unstable/main i386 libcurl3t64-gnutls i386 8.10.1-1 [400 kB] Get: 77 http://deb.debian.org/debian unstable/main i386 libdeflate0 i386 1.21-1 [48.0 kB] Get: 78 http://deb.debian.org/debian unstable/main i386 libgfortran5 i386 14.2.0-5 [735 kB] Get: 79 http://deb.debian.org/debian unstable/main i386 libhtscodecs2 i386 1.6.1-1 [70.8 kB] Get: 80 http://deb.debian.org/debian unstable/main i386 libhts3t64 i386 1.20+ds-1 [495 kB] Get: 81 http://deb.debian.org/debian unstable/main i386 liblapack3 i386 3.12.0-3 [2167 kB] Get: 82 http://deb.debian.org/debian unstable/main i386 libncurses6 i386 6.5-2 [111 kB] Get: 83 http://deb.debian.org/debian unstable/main i386 python3-all i386 3.12.6-1 [1040 B] Get: 84 http://deb.debian.org/debian unstable/main i386 python3-attr all 24.2.0-1 [68.4 kB] Get: 85 http://deb.debian.org/debian unstable/main i386 python3-six all 1.16.0-7 [16.4 kB] Get: 86 http://deb.debian.org/debian unstable/main i386 python3-dateutil all 2.9.0-2 [79.4 kB] Get: 87 http://deb.debian.org/debian unstable/main i386 python3-execnet all 2.1.1-1 [40.2 kB] Get: 88 http://deb.debian.org/debian unstable/main i386 python3-sortedcontainers all 2.4.0-2 [31.9 kB] Get: 89 http://deb.debian.org/debian unstable/main i386 python3-hypothesis all 6.112.0-1 [320 kB] Get: 90 http://deb.debian.org/debian unstable/main i386 python3-iniconfig all 1.1.1-2 [6396 B] Get: 91 http://deb.debian.org/debian unstable/main i386 python3-natsort all 8.0.2-2 [39.0 kB] Get: 92 http://deb.debian.org/debian unstable/main i386 python3-numpy i386 1:1.26.4+ds-11 [4299 kB] Get: 93 http://deb.debian.org/debian unstable/main i386 python3-ncls i386 0.0.63-hotfix+ds-1+b5 [369 kB] Get: 94 http://deb.debian.org/debian unstable/main i386 python3-packaging all 24.1-1 [45.8 kB] Get: 95 http://deb.debian.org/debian unstable/main i386 python3-tz all 2024.1-2 [30.9 kB] Get: 96 http://deb.debian.org/debian unstable/main i386 python3-pandas-lib i386 2.2.2+dfsg-4+b1 [3998 kB] Get: 97 http://deb.debian.org/debian unstable/main i386 python3-pandas all 2.2.2+dfsg-4 [3095 kB] Get: 98 http://deb.debian.org/debian unstable/main i386 python3-pluggy all 1.5.0-1 [26.9 kB] Get: 99 http://deb.debian.org/debian unstable/main i386 python3-tabulate all 0.9.0-1 [45.9 kB] Get: 100 http://deb.debian.org/debian unstable/main i386 python3-pyrle i386 0.0.33-4.1+b1 [279 kB] Get: 101 http://deb.debian.org/debian unstable/main i386 python3-pytest all 8.3.3-1 [249 kB] Get: 102 http://deb.debian.org/debian unstable/main i386 python3-pytest-xdist all 3.6.1-1 [44.4 kB] Get: 103 http://deb.debian.org/debian unstable/main i386 python3-sorted-nearest i386 0.0.39+dfsg-2+b1 [300 kB] Get: 104 http://deb.debian.org/debian unstable/main i386 samtools i386 1.20-3 [688 kB] Fetched 48.8 MB in 3s (18.2 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-minimal:i386. 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Preparing to unpack .../python3.12-minimal_3.12.6-1_i386.deb ... Unpacking python3.12-minimal (3.12.6-1) ... Setting up libpython3.12-minimal:i386 (3.12.6-1) ... Setting up libexpat1:i386 (2.6.3-1) ... Setting up python3.12-minimal (3.12.6-1) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20094 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.6-1_i386.deb ... Unpacking python3-minimal (3.12.6-1) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../03-tzdata_2024a-4_all.deb ... Unpacking tzdata (2024a-4) ... Selecting previously unselected package libkrb5support0:i386. Preparing to unpack .../04-libkrb5support0_1.21.3-3_i386.deb ... Unpacking libkrb5support0:i386 (1.21.3-3) ... Selecting previously unselected package libcom-err2:i386. Preparing to unpack .../05-libcom-err2_1.47.1-1_i386.deb ... Unpacking libcom-err2:i386 (1.47.1-1) ... Selecting previously unselected package libk5crypto3:i386. Preparing to unpack .../06-libk5crypto3_1.21.3-3_i386.deb ... Unpacking libk5crypto3:i386 (1.21.3-3) ... 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Adding 'diversion of /lib/i386-linux-gnu/libtirpc.so.3 to /lib/i386-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/i386-linux-gnu/libtirpc.so.3.0.0 to /lib/i386-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:i386 (1.3.4+ds-1.3) ... Selecting previously unselected package libnsl2:i386. Preparing to unpack .../12-libnsl2_1.3.0-3+b2_i386.deb ... Unpacking libnsl2:i386 (1.3.0-3+b2) ... Selecting previously unselected package readline-common. Preparing to unpack .../13-readline-common_8.2-5_all.deb ... Unpacking readline-common (8.2-5) ... Selecting previously unselected package libreadline8t64:i386. Preparing to unpack .../14-libreadline8t64_8.2-5_i386.deb ... Adding 'diversion of /lib/i386-linux-gnu/libhistory.so.8 to /lib/i386-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/i386-linux-gnu/libhistory.so.8.2 to /lib/i386-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/i386-linux-gnu/libreadline.so.8 to /lib/i386-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/i386-linux-gnu/libreadline.so.8.2 to /lib/i386-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:i386 (8.2-5) ... Selecting previously unselected package libpython3.12-stdlib:i386. Preparing to unpack .../15-libpython3.12-stdlib_3.12.6-1_i386.deb ... Unpacking libpython3.12-stdlib:i386 (3.12.6-1) ... Selecting previously unselected package python3.12. Preparing to unpack .../16-python3.12_3.12.6-1_i386.deb ... Unpacking python3.12 (3.12.6-1) ... Selecting previously unselected package libpython3-stdlib:i386. 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Setting up libtirpc-common (1.3.4+ds-1.3) ... Setting up libdebhelper-perl (13.20) ... Setting up libbrotli1:i386 (1.1.0-2+b4) ... Setting up libmagic1t64:i386 (1:5.45-3) ... Setting up libpsl5t64:i386 (0.21.2-1.1) ... Setting up libnghttp2-14:i386 (1.63.0-1) ... Setting up libdeflate0:i386 (1.21-1) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up libcom-err2:i386 (1.47.1-1) ... Setting up file (1:5.45-3) ... Setting up libelf1t64:i386 (0.191-2) ... Setting up libkrb5support0:i386 (1.21.3-3) ... Setting up libsasl2-modules-db:i386 (2.1.28+dfsg1-8) ... Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' Local time is now: Sat Sep 21 18:56:04 UTC 2024. Universal Time is now: Sat Sep 21 18:56:04 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... Setting up libblas3:i386 (3.12.0-3) ... update-alternatives: using /usr/lib/i386-linux-gnu/blas/libblas.so.3 to provide /usr/lib/i386-linux-gnu/libblas.so.3 (libblas.so.3-i386-linux-gnu) in auto mode Setting up librtmp1:i386 (2.4+20151223.gitfa8646d.1-2+b4) ... Setting up libncurses6:i386 (6.5-2) ... Setting up autopoint (0.22.5-2) ... Setting up libk5crypto3:i386 (1.21.3-3) ... Setting up libsasl2-2:i386 (2.1.28+dfsg1-8) ... Setting up libgfortran5:i386 (14.2.0-5) ... Setting up autoconf (2.72-3) ... Setting up libnghttp3-9:i386 (1.4.0-1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:i386 (0.0.8-1+b1) ... Setting up netbase (6.4) ... Setting up libngtcp2-16:i386 (1.6.0-1) ... Setting up libkrb5-3:i386 (1.21.3-3) ... Setting up libssh2-1t64:i386 (1.11.0-7) ... Setting up readline-common (8.2-5) ... Setting up libxml2:i386 (2.12.7+dfsg-3+b1) ... Setting up bedtools (2.31.1+dfsg-2) ... Setting up libngtcp2-crypto-gnutls8:i386 (1.6.0-1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up liblapack3:i386 (3.12.0-3) ... update-alternatives: using /usr/lib/i386-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/i386-linux-gnu/liblapack.so.3 (liblapack.so.3-i386-linux-gnu) in auto mode Setting up gettext (0.22.5-2) ... Setting up libtool (2.4.7-7) ... Setting up libldap-2.5-0:i386 (2.5.18+dfsg-3) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libgssapi-krb5-2:i386 (1.21.3-3) ... Setting up libreadline8t64:i386 (8.2-5) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... Setting up libtirpc3t64:i386 (1.3.4+ds-1.3) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libcurl3t64-gnutls:i386 (8.10.1-1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libnsl2:i386 (1.3.0-3+b2) ... Setting up libhts3t64:i386 (1.20+ds-1) ... Setting up libpython3.12-stdlib:i386 (3.12.6-1) ... Setting up python3.12 (3.12.6-1) ... Setting up debhelper (13.20) ... Setting up samtools (1.20-3) ... Setting up libpython3-stdlib:i386 (3.12.6-1) ... Setting up python3 (3.12.6-1) ... Setting up python3-sortedcontainers (2.4.0-2) ... Setting up python3-zipp (3.20.2-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up python3-tz (2024.1-2) ... Setting up python3-natsort (8.0.2-2) ... Setting up python3-six (1.16.0-7) ... Setting up python3-packaging (24.1-1) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up python3-pluggy (1.5.0-1) ... Setting up python3-dateutil (2.9.0-2) ... Setting up python3-execnet (2.1.1-1) ... Setting up python3-more-itertools (10.4.0-1) ... Setting up python3-iniconfig (1.1.1-2) ... Setting up python3-attr (24.2.0-1) ... Setting up python3-jaraco.functools (4.0.2-1) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up python3-pytest (8.3.3-1) ... Setting up python3-hypothesis (6.112.0-1) ... Setting up python3-typeguard (4.3.0-1) ... Setting up python3-tabulate (0.9.0-1) ... Setting up python3-all (3.12.6-1) ... Setting up python3-inflect (7.3.1-2) ... Setting up python3-pkg-resources (74.1.2-2) ... Setting up python3-setuptools (74.1.2-2) ... Setting up python3-pytest-xdist (3.6.1-1) ... Setting up python3-numpy (1:1.26.4+ds-11) ... Setting up python3-ncls (0.0.63-hotfix+ds-1+b5) ... Setting up dh-python (6.20240824) ... Setting up python3-pandas-lib:i386 (2.2.2+dfsg-4+b1) ... Setting up python3-sorted-nearest (0.0.39+dfsg-2+b1) ... Setting up python3-pandas (2.2.2+dfsg-4) ... Setting up python3-pyrle (0.0.33-4.1+b1) ... Processing triggers for libc-bin (2.40-2) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/pyranges-0.0.111+ds/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../pyranges_0.0.111+ds-8_source.changes dpkg-buildpackage: info: source package pyranges dpkg-buildpackage: info: source version 0.0.111+ds-8 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 dpkg-source: info: using options from pyranges-0.0.111+ds/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/ debian/rules clean dh clean --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild I: pybuild base:311: python3.12 setup.py clean 'build/bdist.linux-i686' does not exist -- can't clean it 'build/scripts-3.12' does not exist -- can't clean it dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:311: python3.12 setup.py config dh_auto_build -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3 setup.py build debian/rules execute_after_dh_auto_build make[1]: Entering directory '/build/reproducible-path/pyranges-0.0.111+ds' echo 'Generating corresponding files ...' Generating corresponding files ... cat debian/missing-sources/test_sorted.sam| samtools view -Sb - > tests/test_data/test_sorted.bam cat debian/missing-sources/control.sam| samtools view -Sb - > pyranges/example_data/control.bam samtools index tests/test_data/test_sorted.bam tests/test_data/test_sorted.bam.bai samtools index pyranges/example_data/control.bam pyranges/example_data/control.bam.bai make[1]: Leaving directory '/build/reproducible-path/pyranges-0.0.111+ds' dh_auto_test -O--buildsystem=pybuild I: pybuild pybuild:308: mkdir -pv /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges && cp -av /build/reproducible-path/pyranges-0.0.111+ds/tests/*.bed /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests && cp -av /build/reproducible-path/pyranges-0.0.111+ds/tests/test_data /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests && cp -av /build/reproducible-path/pyranges-0.0.111+ds/tests/data /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests && cp -av /build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges '/build/reproducible-path/pyranges-0.0.111+ds/tests/chip_10.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/chip_10.bed' '/build/reproducible-path/pyranges-0.0.111+ds/tests/f1.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/f1.bed' '/build/reproducible-path/pyranges-0.0.111+ds/tests/f2.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/f2.bed' '/build/reproducible-path/pyranges-0.0.111+ds/tests/test_data' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_data' '/build/reproducible-path/pyranges-0.0.111+ds/tests/test_data/ensembl.gtf' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_data/ensembl.gtf' '/build/reproducible-path/pyranges-0.0.111+ds/tests/test_data/gencode.gff3' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_data/gencode.gff3' '/build/reproducible-path/pyranges-0.0.111+ds/tests/test_data/ucsc_df_to_parse.txt' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_data/ucsc_df_to_parse.txt' '/build/reproducible-path/pyranges-0.0.111+ds/tests/test_data/test_sorted.bam' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_data/test_sorted.bam' '/build/reproducible-path/pyranges-0.0.111+ds/tests/test_data/test_sorted.bam.bai' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_data/test_sorted.bam.bai' '/build/reproducible-path/pyranges-0.0.111+ds/tests/data' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/data' '/build/reproducible-path/pyranges-0.0.111+ds/tests/data/test_data.py' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/data/test_data.py' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/exons.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/example_data/exons.bed' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/ensembl.gtf' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/example_data/ensembl.gtf' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/ucsc_human.bed.gz' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/example_data/ucsc_human.bed.gz' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/chipseq_background.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/example_data/chipseq_background.bed' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/f2.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/example_data/f2.bed' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/bw.bw' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/example_data/bw.bw' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/f1.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/example_data/f1.bed' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/cpg.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/example_data/cpg.bed' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/lamina.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/example_data/lamina.bed' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/gencode_human.gtf.gz' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/example_data/gencode_human.gtf.gz' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/chipseq.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/example_data/chipseq.bed' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/aorta.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/example_data/aorta.bed' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/ensembl_human.gtf.gz' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/example_data/ensembl_human.gtf.gz' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/chromsizes.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/example_data/chromsizes.bed' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/aorta2.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/example_data/aorta2.bed' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/control.bam' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/example_data/control.bam' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/control.bam.bai' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/example_data/control.bam.bai' I: pybuild base:311: cd /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build; python3.12 -m pytest -v -n 11 ============================= test session starts ============================== platform linux -- Python 3.12.6, pytest-8.3.3, pluggy-1.5.0 -- /usr/bin/python3.12 cachedir: .pytest_cache hypothesis profile 'default' -> database=DirectoryBasedExampleDatabase(PosixPath('/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/.hypothesis/examples')) rootdir: /build/reproducible-path/pyranges-0.0.111+ds plugins: xdist-3.6.1, typeguard-4.3.0, hypothesis-6.112.0 created: 11/11 workers 11 workers [531 items] scheduling tests via LoadScheduling tests/data/test_data.py::test_all_data tests/test_binary.py::test_jaccard[same] tests/test_binary.py::test_nearest[upstream-True-same] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain7-method_chain7] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain55-method_chain55] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain31-method_chain31] tests/test_binary.py::test_k_nearest[upstream-False-same-last] tests/test_binary.py::test_coverage[same] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain43-method_chain43] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain19-method_chain19] tests/test_change_chromosome_custom.py::test_change_chromosomes [gw5] [ 0%] PASSED tests/test_change_chromosome_custom.py::test_change_chromosomes tests/test_concat.py::test_concat_stranded_unstranded [gw5] [ 0%] PASSED tests/test_concat.py::test_concat_stranded_unstranded tests/test_concat.py::test_concat_unstranded_unstranded [gw5] [ 0%] PASSED tests/test_concat.py::test_concat_unstranded_unstranded tests/test_concat.py::test_concat_unstranded_stranded [gw5] [ 0%] PASSED tests/test_concat.py::test_concat_unstranded_stranded tests/test_count_overlaps.py::test_strand_vs_strand_same [gw5] [ 0%] PASSED tests/test_count_overlaps.py::test_strand_vs_strand_same tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain0-method_chain0] [gw0] [ 1%] PASSED tests/data/test_data.py::test_all_data tests/test_binary.py::test_set_intersect[False] [gw4] [ 1%] FAILED tests/test_binary.py::test_k_nearest[upstream-False-same-last] tests/test_binary.py::test_k_nearest[upstream-False-False-last] [gw9] [ 1%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain55-method_chain55] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain56-method_chain56] [gw4] [ 1%] FAILED tests/test_binary.py::test_k_nearest[upstream-False-False-last] tests/test_binary.py::test_k_nearest[upstream-True-opposite-last] [gw6] [ 1%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain19-method_chain19] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain20-method_chain20] [gw6] [ 2%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain20-method_chain20] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain21-method_chain21] [gw10] [ 2%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain43-method_chain43] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain44-method_chain44] [gw7] [ 2%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain7-method_chain7] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain8-method_chain8] [gw10] [ 2%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain44-method_chain44] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain45-method_chain45] [gw5] [ 2%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain0-method_chain0] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain1-method_chain1] [gw3] [ 3%] FAILED tests/test_binary.py::test_jaccard[same] tests/test_binary.py::test_join[False] [gw2] [ 3%] FAILED tests/test_binary.py::test_nearest[upstream-True-same] tests/test_binary.py::test_nearest[upstream-True-opposite] [gw0] [ 3%] FAILED tests/test_binary.py::test_set_intersect[False] [gw1] [ 3%] FAILED tests/test_binary.py::test_coverage[same] tests/test_binary.py::test_set_intersect[same] tests/test_binary.py::test_coverage[opposite] [gw8] [ 3%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain31-method_chain31] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain32-method_chain32] [gw8] [ 3%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain32-method_chain32] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain33-method_chain33] [gw9] [ 4%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain56-method_chain56] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain57-method_chain57] [gw4] [ 4%] FAILED tests/test_binary.py::test_k_nearest[upstream-True-opposite-last] tests/test_binary.py::test_k_nearest[upstream-True-same-last] [gw7] [ 4%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain8-method_chain8] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain9-method_chain9] [gw8] [ 4%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain33-method_chain33] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain34-method_chain34] [gw5] [ 4%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain1-method_chain1] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain2-method_chain2] [gw8] [ 5%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain34-method_chain34] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain35-method_chain35] [gw6] [ 5%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain21-method_chain21] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain22-method_chain22] [gw3] [ 5%] PASSED tests/test_binary.py::test_join[False] tests/test_binary.py::test_join[same] [gw4] [ 5%] FAILED tests/test_binary.py::test_k_nearest[upstream-True-same-last] tests/test_binary.py::test_k_nearest[upstream-True-False-last] [gw10] [ 5%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain45-method_chain45] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain46-method_chain46] [gw0] [ 6%] FAILED tests/test_binary.py::test_set_intersect[same] tests/test_binary.py::test_set_union[False] [gw9] [ 6%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain57-method_chain57] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain58-method_chain58] [gw2] [ 6%] FAILED tests/test_binary.py::test_nearest[upstream-True-opposite] tests/test_binary.py::test_nearest[upstream-False-False] [gw7] [ 6%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain9-method_chain9] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain10-method_chain10] [gw10] [ 6%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain46-method_chain46] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain47-method_chain47] [gw1] [ 6%] FAILED tests/test_binary.py::test_coverage[opposite] tests/test_binary.py::test_subtraction[same] [gw5] [ 7%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain2-method_chain2] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain3-method_chain3] [gw4] [ 7%] FAILED tests/test_binary.py::test_k_nearest[upstream-True-False-last] tests/test_binary.py::test_k_nearest[None-False-opposite-last] [gw2] [ 7%] FAILED tests/test_binary.py::test_nearest[upstream-False-False] tests/test_binary.py::test_nearest[upstream-False-same] [gw9] [ 7%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain58-method_chain58] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain59-method_chain59] [gw7] [ 7%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain10-method_chain10] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain11-method_chain11] [gw4] [ 8%] FAILED tests/test_binary.py::test_k_nearest[None-False-opposite-last] tests/test_binary.py::test_k_nearest[None-False-same-last] [gw3] [ 8%] PASSED tests/test_binary.py::test_join[same] tests/test_binary.py::test_join[opposite] [gw10] [ 8%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain47-method_chain47] [gw8] [ 8%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain35-method_chain35] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain48-method_chain48] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain36-method_chain36] [gw4] [ 8%] FAILED tests/test_binary.py::test_k_nearest[None-False-same-last] tests/test_binary.py::test_k_nearest[None-False-False-last] [gw2] [ 9%] FAILED tests/test_binary.py::test_nearest[upstream-False-same] tests/test_binary.py::test_nearest[upstream-False-opposite] [gw10] [ 9%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain48-method_chain48] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain49-method_chain49] [gw5] [ 9%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain3-method_chain3] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain4-method_chain4] [gw6] [ 9%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain22-method_chain22] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain23-method_chain23] [gw9] [ 9%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain59-method_chain59] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain60-method_chain60] [gw4] [ 9%] FAILED tests/test_binary.py::test_k_nearest[None-False-False-last] tests/test_binary.py::test_k_nearest[None-True-opposite-last] [gw1] [ 10%] FAILED tests/test_binary.py::test_subtraction[same] tests/test_binary.py::test_subtraction[opposite] [gw7] [ 10%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain11-method_chain11] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain12-method_chain12] [gw0] [ 10%] FAILED tests/test_binary.py::test_set_union[False] tests/test_binary.py::test_set_union[same] [gw3] [ 10%] PASSED tests/test_binary.py::test_join[opposite] tests/test_binary.py::test_reldist [gw9] [ 10%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain60-method_chain60] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain61-method_chain61] [gw2] [ 11%] FAILED tests/test_binary.py::test_nearest[upstream-False-opposite] tests/test_binary.py::test_nearest[downstream-True-False] [gw5] [ 11%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain4-method_chain4] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain5-method_chain5] [gw4] [ 11%] FAILED tests/test_binary.py::test_k_nearest[None-True-opposite-last] tests/test_binary.py::test_k_nearest[None-True-same-last] [gw4] [ 11%] FAILED tests/test_binary.py::test_k_nearest[None-True-same-last] tests/test_binary.py::test_k_nearest[None-True-False-last] [gw10] [ 11%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain49-method_chain49] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain50-method_chain50] [gw8] [ 12%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain36-method_chain36] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain37-method_chain37] [gw4] [ 12%] FAILED tests/test_binary.py::test_k_nearest[None-True-False-last] tests/test_binary.py::test_k_nearest_1_vs_nearest [gw4] [ 12%] FAILED tests/test_binary.py::test_k_nearest_1_vs_nearest tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain77-method_chain77] [gw3] [ 12%] PASSED tests/test_binary.py::test_reldist tests/test_binary.py::test_k_nearest[downstream-False-opposite-last] [gw7] [ 12%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain12-method_chain12] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain13-method_chain13] [gw2] [ 12%] FAILED tests/test_binary.py::test_nearest[downstream-True-False] tests/test_binary.py::test_nearest[downstream-True-same] [gw6] [ 13%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain23-method_chain23] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain24-method_chain24] [gw9] [ 13%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain61-method_chain61] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain62-method_chain62] [gw1] [ 13%] FAILED tests/test_binary.py::test_subtraction[opposite] tests/test_binary.py::test_subtraction[False] [gw0] [ 13%] FAILED tests/test_binary.py::test_set_union[same] [gw8] [ 13%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain37-method_chain37] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain38-method_chain38] tests/test_binary.py::test_overlap[False] [gw5] [ 14%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain5-method_chain5] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain6-method_chain6] [gw7] [ 14%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain13-method_chain13] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain14-method_chain14] [gw4] [ 14%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain77-method_chain77] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain78-method_chain78] [gw10] [ 14%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain50-method_chain50] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain51-method_chain51] [gw9] [ 14%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain62-method_chain62] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain63-method_chain63] [gw3] [ 15%] FAILED tests/test_binary.py::test_k_nearest[downstream-False-opposite-last] tests/test_binary.py::test_k_nearest[downstream-False-same-last] [gw6] [ 15%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain24-method_chain24] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain25-method_chain25] [gw2] [ 15%] FAILED tests/test_binary.py::test_nearest[downstream-True-same] tests/test_binary.py::test_nearest[downstream-True-opposite] [gw10] [ 15%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain51-method_chain51] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain52-method_chain52] [gw1] [ 15%] FAILED tests/test_binary.py::test_subtraction[False] tests/test_binary.py::test_nearest[None-True-False] [gw0] [ 16%] PASSED tests/test_binary.py::test_overlap[False] tests/test_binary.py::test_overlap[same] [gw5] [ 16%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain6-method_chain6] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain67-method_chain67] [gw4] [ 16%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain78-method_chain78] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain79-method_chain79] [gw7] [ 16%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain14-method_chain14] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain15-method_chain15] [gw5] [ 16%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain67-method_chain67] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain68-method_chain68] [gw9] [ 16%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain63-method_chain63] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain64-method_chain64] [gw8] [ 17%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain38-method_chain38] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain39-method_chain39] [gw4] [ 17%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain79-method_chain79] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain80-method_chain80] [gw3] [ 17%] FAILED tests/test_binary.py::test_k_nearest[downstream-False-same-last] tests/test_binary.py::test_k_nearest[downstream-False-False-last] [gw10] [ 17%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain52-method_chain52] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain53-method_chain53] [gw1] [ 17%] FAILED tests/test_binary.py::test_nearest[None-True-False] tests/test_binary.py::test_nearest[None-True-same] [gw2] [ 18%] FAILED tests/test_binary.py::test_nearest[downstream-True-opposite] tests/test_binary.py::test_nearest[downstream-False-False] [gw6] [ 18%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain25-method_chain25] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain26-method_chain26] [gw5] [ 18%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain68-method_chain68] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain69-method_chain69] [gw9] [ 18%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain64-method_chain64] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain65-method_chain65] [gw3] [ 18%] FAILED tests/test_binary.py::test_k_nearest[downstream-False-False-last] tests/test_binary.py::test_k_nearest[downstream-True-opposite-last] [gw7] [ 19%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain15-method_chain15] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain16-method_chain16] [gw5] [ 19%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain69-method_chain69] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain70-method_chain70] [gw9] [ 19%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain65-method_chain65] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain66-method_chain66] [gw0] [ 19%] PASSED tests/test_binary.py::test_overlap[same] [gw7] [ 19%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain16-method_chain16] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain17-method_chain17] tests/test_binary.py::test_overlap[opposite] [gw8] [ 19%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain39-method_chain39] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain40-method_chain40] [gw10] [ 20%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain53-method_chain53] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain54-method_chain54] [gw2] [ 20%] FAILED tests/test_binary.py::test_nearest[downstream-False-False] tests/test_binary.py::test_nearest[downstream-False-same] [gw4] [ 20%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain80-method_chain80] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain81-method_chain81] [gw4] [ 20%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain81-method_chain81] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain82-method_chain82] [gw1] [ 20%] FAILED tests/test_binary.py::test_nearest[None-True-same] tests/test_binary.py::test_nearest[None-True-opposite] [gw3] [ 21%] FAILED tests/test_binary.py::test_k_nearest[downstream-True-opposite-last] tests/test_binary.py::test_k_nearest[downstream-True-same-last] [gw6] [ 21%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain26-method_chain26] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain27-method_chain27] [gw8] [ 21%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain40-method_chain40] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain41-method_chain41] [gw3] [ 21%] FAILED tests/test_binary.py::test_k_nearest[downstream-True-same-last] tests/test_binary.py::test_k_nearest[downstream-True-False-last] [gw7] [ 21%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain17-method_chain17] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain18-method_chain18] [gw5] [ 22%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain70-method_chain70] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain71-method_chain71] [gw7] [ 22%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain18-method_chain18] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain123-method_chain123] [gw10] [ 22%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain54-method_chain54] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain108-method_chain108] [gw2] [ 22%] FAILED tests/test_binary.py::test_nearest[downstream-False-same] tests/test_binary.py::test_nearest[downstream-False-opposite] [gw9] [ 22%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain66-method_chain66] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain93-method_chain93] [gw0] [ 22%] PASSED tests/test_binary.py::test_overlap[opposite] tests/test_binary.py::test_intersect[False] [gw9] [ 23%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain93-method_chain93] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain94-method_chain94] [gw4] [ 23%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain82-method_chain82] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain83-method_chain83] [gw4] [ 23%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain83-method_chain83] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain84-method_chain84] [gw1] [ 23%] FAILED tests/test_binary.py::test_nearest[None-True-opposite] tests/test_binary.py::test_nearest[None-False-False] [gw3] [ 23%] FAILED tests/test_binary.py::test_k_nearest[downstream-True-False-last] tests/test_binary.py::test_k_nearest[upstream-False-opposite-last] [gw6] [ 24%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain27-method_chain27] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain28-method_chain28] [gw8] [ 24%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain41-method_chain41] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain42-method_chain42] [gw1] [ 24%] FAILED tests/test_binary.py::test_nearest[None-False-False] tests/test_binary.py::test_nearest[None-False-same] [gw5] [ 24%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain71-method_chain71] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain72-method_chain72] [gw10] [ 24%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain108-method_chain108] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain109-method_chain109] [gw7] [ 25%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain123-method_chain123] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain124-method_chain124] [gw2] [ 25%] FAILED tests/test_binary.py::test_nearest[downstream-False-opposite] tests/test_binary.py::test_jaccard[False] [gw1] [ 25%] FAILED tests/test_binary.py::test_nearest[None-False-same] tests/test_binary.py::test_nearest[None-False-opposite] [gw9] [ 25%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain94-method_chain94] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain95-method_chain95] [gw4] [ 25%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain84-method_chain84] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain85-method_chain85] [gw9] [ 25%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain95-method_chain95] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain96-method_chain96] [gw3] [ 26%] FAILED tests/test_binary.py::test_k_nearest[upstream-False-opposite-last] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain137-method_chain137] [gw0] [ 26%] PASSED tests/test_binary.py::test_intersect[False] tests/test_binary.py::test_intersect[same] [gw1] [ 26%] FAILED tests/test_binary.py::test_nearest[None-False-opposite] tests/test_binary.py::test_nearest[upstream-True-False] [gw6] [ 26%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain28-method_chain28] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain29-method_chain29] [gw10] [ 26%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain109-method_chain109] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain110-method_chain110] [gw8] [ 27%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain42-method_chain42] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain150-method_chain150] [gw2] [ 27%] FAILED tests/test_binary.py::test_jaccard[False] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain163-method_chain163] [gw5] [ 27%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain72-method_chain72] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain73-method_chain73] [gw7] [ 27%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain124-method_chain124] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain125-method_chain125] [gw2] [ 27%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain163-method_chain163] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain164-method_chain164] [gw9] [ 28%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain96-method_chain96] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain97-method_chain97] [gw9] [ 28%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain97-method_chain97] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain98-method_chain98] [gw4] [ 28%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain85-method_chain85] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain86-method_chain86] [gw1] [ 28%] FAILED tests/test_binary.py::test_nearest[upstream-True-False] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain175-method_chain175] [gw3] [ 28%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain137-method_chain137] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain138-method_chain138] [gw8] [ 29%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain150-method_chain150] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain151-method_chain151] [gw6] [ 29%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain29-method_chain29] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain30-method_chain30] [gw6] [ 29%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain30-method_chain30] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain187-method_chain187] [gw0] [ 29%] PASSED tests/test_binary.py::test_intersect[same] tests/test_binary.py::test_intersect[opposite] [gw10] [ 29%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain110-method_chain110] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain111-method_chain111] [gw5] [ 29%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain73-method_chain73] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain74-method_chain74] [gw8] [ 30%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain151-method_chain151] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain152-method_chain152] [gw3] [ 30%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain138-method_chain138] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain139-method_chain139] [gw7] [ 30%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain125-method_chain125] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain126-method_chain126] [gw4] [ 30%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain86-method_chain86] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain87-method_chain87] [gw2] [ 30%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain164-method_chain164] [gw1] [ 31%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain175-method_chain175] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain165-method_chain165] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain176-method_chain176] [gw2] [ 31%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain165-method_chain165] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain166-method_chain166] [gw9] [ 31%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain98-method_chain98] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain99-method_chain99] [gw10] [ 31%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain111-method_chain111] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain112-method_chain112] [gw0] [ 31%] PASSED tests/test_binary.py::test_intersect[opposite] tests/test_binary.py::test_coverage[False] [gw7] [ 32%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain126-method_chain126] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain127-method_chain127] [gw6] [ 32%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain187-method_chain187] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain188-method_chain188] [gw1] [ 32%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain176-method_chain176] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain177-method_chain177] [gw1] [ 32%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain177-method_chain177] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain178-method_chain178] [gw2] [ 32%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain166-method_chain166] [gw5] [ 32%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain74-method_chain74] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain75-method_chain75] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain167-method_chain167] [gw8] [ 33%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain152-method_chain152] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain153-method_chain153] [gw3] [ 33%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain139-method_chain139] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain140-method_chain140] [gw2] [ 33%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain167-method_chain167] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain168-method_chain168] [gw10] [ 33%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain112-method_chain112] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain113-method_chain113] [gw4] [ 33%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain87-method_chain87] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain88-method_chain88] [gw9] [ 34%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain99-method_chain99] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain100-method_chain100] [gw7] [ 34%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain127-method_chain127] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain128-method_chain128] [gw7] [ 34%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain128-method_chain128] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain129-method_chain129] [gw6] [ 34%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain188-method_chain188] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain189-method_chain189] [gw0] [ 34%] FAILED tests/test_binary.py::test_coverage[False] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain198-method_chain198] [gw8] [ 35%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain153-method_chain153] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain154-method_chain154] [gw9] [ 35%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain100-method_chain100] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain101-method_chain101] [gw3] [ 35%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain140-method_chain140] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain141-method_chain141] [gw10] [ 35%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain113-method_chain113] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain114-method_chain114] [gw10] [ 35%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain114-method_chain114] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain115-method_chain115] [gw1] [ 35%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain178-method_chain178] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain179-method_chain179] [gw4] [ 36%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain88-method_chain88] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain89-method_chain89] [gw5] [ 36%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain75-method_chain75] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain76-method_chain76] [gw0] [ 36%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain198-method_chain198] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain199-method_chain199] [gw1] [ 36%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain179-method_chain179] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain180-method_chain180] [gw2] [ 36%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain168-method_chain168] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain169-method_chain169] [gw6] [ 37%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain189-method_chain189] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain190-method_chain190] [gw9] [ 37%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain101-method_chain101] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain102-method_chain102] [gw7] [ 37%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain129-method_chain129] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain130-method_chain130] [gw8] [ 37%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain154-method_chain154] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain155-method_chain155] [gw7] [ 37%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain130-method_chain130] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain131-method_chain131] [gw3] [ 38%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain141-method_chain141] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain142-method_chain142] [gw0] [ 38%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain199-method_chain199] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain200-method_chain200] [gw4] [ 38%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain89-method_chain89] [gw3] [ 38%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain142-method_chain142] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain90-method_chain90] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain143-method_chain143] [gw1] [ 38%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain180-method_chain180] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain181-method_chain181] [gw1] [ 38%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain181-method_chain181] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain182-method_chain182] [gw9] [ 39%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain102-method_chain102] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain103-method_chain103] [gw6] [ 39%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain190-method_chain190] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain191-method_chain191] [gw7] [ 39%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain131-method_chain131] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain132-method_chain132] [gw5] [ 39%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain76-method_chain76] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain209-method_chain209] [gw6] [ 39%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain191-method_chain191] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain192-method_chain192] [gw7] [ 40%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain132-method_chain132] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain133-method_chain133] [gw10] [ 40%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain115-method_chain115] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain116-method_chain116] [gw0] [ 40%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain200-method_chain200] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain201-method_chain201] [gw2] [ 40%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain169-method_chain169] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain170-method_chain170] [gw10] [ 40%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain116-method_chain116] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain117-method_chain117] [gw8] [ 41%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain155-method_chain155] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain156-method_chain156] [gw4] [ 41%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain90-method_chain90] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain91-method_chain91] [gw3] [ 41%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain143-method_chain143] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain144-method_chain144] [gw5] [ 41%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain209-method_chain209] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain210-method_chain210] [gw3] [ 41%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain144-method_chain144] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain145-method_chain145] [gw8] [ 41%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain156-method_chain156] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain157-method_chain157] [gw9] [ 42%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain103-method_chain103] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain104-method_chain104] [gw1] [ 42%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain182-method_chain182] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain183-method_chain183] [gw10] [ 42%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain117-method_chain117] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain118-method_chain118] [gw10] [ 42%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain118-method_chain118] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain119-method_chain119] [gw0] [ 42%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain201-method_chain201] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain202-method_chain202] [gw7] [ 43%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain133-method_chain133] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain134-method_chain134] [gw6] [ 43%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain192-method_chain192] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain193-method_chain193] [gw2] [ 43%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain170-method_chain170] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain171-method_chain171] [gw8] [ 43%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain157-method_chain157] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain158-method_chain158] [gw6] [ 43%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain193-method_chain193] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain194-method_chain194] [gw9] [ 44%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain104-method_chain104] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain105-method_chain105] [gw4] [ 44%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain91-method_chain91] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain92-method_chain92] [gw5] [ 44%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain210-method_chain210] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain211-method_chain211] [gw3] [ 44%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain145-method_chain145] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain146-method_chain146] [gw0] [ 44%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain202-method_chain202] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain203-method_chain203] [gw3] [ 45%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain146-method_chain146] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain147-method_chain147] [gw1] [ 45%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain183-method_chain183] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain184-method_chain184] [gw8] [ 45%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain158-method_chain158] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain159-method_chain159] [gw5] [ 45%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain211-method_chain211] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain212-method_chain212] [gw6] [ 45%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain194-method_chain194] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain195-method_chain195] [gw5] [ 45%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain212-method_chain212] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain213-method_chain213] [gw6] [ 46%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain195-method_chain195] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain196-method_chain196] [gw7] [ 46%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain134-method_chain134] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain135-method_chain135] [gw9] [ 46%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain105-method_chain105] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain106-method_chain106] [gw10] [ 46%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain119-method_chain119] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain120-method_chain120] [gw1] [ 46%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain184-method_chain184] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain185-method_chain185] [gw4] [ 47%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain92-method_chain92] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain219-method_chain219] [gw2] [ 47%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain171-method_chain171] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain172-method_chain172] [gw0] [ 47%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain203-method_chain203] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain204-method_chain204] [gw3] [ 47%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain147-method_chain147] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain148-method_chain148] [gw8] [ 47%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain159-method_chain159] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain160-method_chain160] [gw7] [ 48%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain135-method_chain135] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain136-method_chain136] [gw6] [ 48%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain196-method_chain196] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain197-method_chain197] [gw9] [ 48%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain106-method_chain106] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain107-method_chain107] [gw5] [ 48%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain213-method_chain213] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain214-method_chain214] [gw5] [ 48%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain214-method_chain214] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain215-method_chain215] [gw8] [ 48%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain160-method_chain160] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain161-method_chain161] [gw0] [ 49%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain204-method_chain204] [gw1] [ 49%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain185-method_chain185] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain205-method_chain205] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain186-method_chain186] [gw3] [ 49%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain148-method_chain148] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain149-method_chain149] [gw10] [ 49%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain120-method_chain120] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain121-method_chain121] [gw4] [ 49%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain219-method_chain219] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain220-method_chain220] [gw2] [ 50%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain172-method_chain172] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain173-method_chain173] [gw9] [ 50%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain107-method_chain107] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain247-method_chain247] [gw6] [ 50%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain197-method_chain197] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain238-method_chain238] [gw7] [ 50%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain136-method_chain136] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain229-method_chain229] [gw3] [ 50%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain149-method_chain149] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain263-method_chain263] [gw0] [ 51%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain205-method_chain205] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain206-method_chain206] [gw8] [ 51%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain161-method_chain161] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain162-method_chain162] [gw3] [ 51%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain263-method_chain263] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain264-method_chain264] [gw1] [ 51%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain186-method_chain186] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain255-method_chain255] [gw5] [ 51%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain215-method_chain215] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain216-method_chain216] [gw5] [ 51%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain216-method_chain216] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain217-method_chain217] [gw9] [ 52%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain247-method_chain247] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain248-method_chain248] [gw6] [ 52%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain238-method_chain238] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain239-method_chain239] [gw0] [ 52%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain206-method_chain206] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain207-method_chain207] [gw10] [ 52%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain121-method_chain121] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain122-method_chain122] [gw4] [ 52%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain220-method_chain220] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain221-method_chain221] [gw8] [ 53%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain162-method_chain162] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain271-method_chain271] [gw7] [ 53%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain229-method_chain229] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain230-method_chain230] [gw3] [ 53%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain264-method_chain264] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain265-method_chain265] [gw7] [ 53%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain230-method_chain230] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain231-method_chain231] [gw2] [ 53%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain173-method_chain173] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain174-method_chain174] [gw3] [ 54%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain265-method_chain265] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain266-method_chain266] [gw9] [ 54%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain248-method_chain248] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain249-method_chain249] [gw1] [ 54%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain255-method_chain255] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain256-method_chain256] [gw6] [ 54%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain239-method_chain239] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain240-method_chain240] [gw6] [ 54%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain240-method_chain240] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain241-method_chain241] [gw0] [ 54%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain207-method_chain207] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain208-method_chain208] [gw1] [ 55%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain256-method_chain256] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain257-method_chain257] [gw9] [ 55%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain249-method_chain249] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain250-method_chain250] [gw5] [ 55%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain217-method_chain217] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain218-method_chain218] [gw2] [ 55%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain174-method_chain174] [gw7] [ 55%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain231-method_chain231] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain285-method_chain285] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain232-method_chain232] [gw4] [ 56%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain221-method_chain221] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain222-method_chain222] [gw10] [ 56%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain122-method_chain122] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain278-method_chain278] [gw8] [ 56%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain271-method_chain271] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain272-method_chain272] [gw9] [ 56%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain250-method_chain250] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain251-method_chain251] [gw3] [ 56%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain266-method_chain266] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain267-method_chain267] [gw0] [ 57%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain208-method_chain208] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain292-method_chain292] [gw1] [ 57%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain257-method_chain257] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain258-method_chain258] [gw2] [ 57%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain285-method_chain285] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain286-method_chain286] [gw6] [ 57%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain241-method_chain241] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain242-method_chain242] [gw6] [ 57%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain242-method_chain242] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain243-method_chain243] [gw10] [ 58%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain278-method_chain278] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain279-method_chain279] [gw10] [ 58%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain279-method_chain279] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain280-method_chain280] [gw9] [ 58%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain251-method_chain251] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain252-method_chain252] [gw5] [ 58%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain218-method_chain218] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain298-method_chain298] [gw0] [ 58%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain292-method_chain292] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain293-method_chain293] [gw7] [ 58%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain232-method_chain232] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain233-method_chain233] [gw0] [ 59%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain293-method_chain293] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain294-method_chain294] [gw1] [ 59%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain258-method_chain258] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain259-method_chain259] [gw4] [ 59%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain222-method_chain222] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain223-method_chain223] [gw8] [ 59%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain272-method_chain272] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain273-method_chain273] [gw5] [ 59%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain298-method_chain298] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain299-method_chain299] [gw6] [ 60%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain243-method_chain243] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain244-method_chain244] [gw3] [ 60%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain267-method_chain267] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain268-method_chain268] [gw6] [ 60%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain244-method_chain244] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain245-method_chain245] [gw2] [ 60%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain286-method_chain286] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain287-method_chain287] [gw7] [ 60%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain233-method_chain233] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain234-method_chain234] [gw9] [ 61%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain252-method_chain252] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain253-method_chain253] [gw1] [ 61%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain259-method_chain259] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain260-method_chain260] [gw10] [ 61%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain280-method_chain280] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain281-method_chain281] [gw0] [ 61%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain294-method_chain294] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain295-method_chain295] [gw8] [ 61%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain273-method_chain273] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain274-method_chain274] [gw5] [ 61%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain299-method_chain299] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain300-method_chain300] [gw4] [ 62%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain223-method_chain223] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain224-method_chain224] [gw6] [ 62%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain245-method_chain245] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain246-method_chain246] [gw1] [ 62%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain260-method_chain260] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain261-method_chain261] [gw2] [ 62%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain287-method_chain287] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain288-method_chain288] [gw9] [ 62%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain253-method_chain253] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain254-method_chain254] [gw1] [ 63%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain261-method_chain261] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain262-method_chain262] [gw3] [ 63%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain268-method_chain268] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain269-method_chain269] [gw8] [ 63%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain274-method_chain274] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain275-method_chain275] [gw0] [ 63%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain295-method_chain295] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain296-method_chain296] [gw8] [ 63%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain275-method_chain275] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain276-method_chain276] [gw10] [ 64%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain281-method_chain281] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain282-method_chain282] [gw7] [ 64%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain234-method_chain234] [gw5] [ 64%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain300-method_chain300] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain235-method_chain235] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain301-method_chain301] [gw9] [ 64%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain254-method_chain254] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain310-method_chain310] [gw0] [ 64%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain296-method_chain296] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain297-method_chain297] [gw9] [ 64%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain310-method_chain310] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain311-method_chain311] [gw4] [ 65%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain224-method_chain224] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain225-method_chain225] [gw6] [ 65%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain246-method_chain246] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain304-method_chain304] [gw2] [ 65%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain288-method_chain288] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain289-method_chain289] [gw10] [ 65%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain282-method_chain282] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain283-method_chain283] [gw2] [ 65%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain289-method_chain289] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain290-method_chain290] [gw7] [ 66%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain235-method_chain235] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain236-method_chain236] [gw0] [ 66%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain297-method_chain297] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain321-method_chain321] [gw5] [ 66%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain301-method_chain301] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain302-method_chain302] [gw3] [ 66%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain269-method_chain269] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain270-method_chain270] [gw4] [ 66%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain225-method_chain225] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain226-method_chain226] [gw1] [ 67%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain262-method_chain262] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain316-method_chain316] [gw6] [ 67%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain304-method_chain304] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain305-method_chain305] [gw4] [ 67%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain226-method_chain226] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain227-method_chain227] [gw8] [ 67%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain276-method_chain276] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain277-method_chain277] [gw8] [ 67%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain277-method_chain277] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain331-method_chain331] [gw6] [ 67%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain305-method_chain305] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain306-method_chain306] [gw7] [ 68%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain236-method_chain236] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain237-method_chain237] [gw9] [ 68%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain311-method_chain311] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain312-method_chain312] [gw5] [ 68%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain302-method_chain302] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain303-method_chain303] [gw8] [ 68%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain331-method_chain331] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain332-method_chain332] [gw9] [ 68%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain312-method_chain312] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain313-method_chain313] [gw0] [ 69%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain321-method_chain321] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain322-method_chain322] [gw2] [ 69%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain290-method_chain290] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain291-method_chain291] [gw10] [ 69%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain283-method_chain283] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain284-method_chain284] [gw2] [ 69%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain291-method_chain291] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain344-method_chain344] [gw3] [ 69%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain270-method_chain270] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain326-method_chain326] [gw5] [ 70%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain303-method_chain303] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain340-method_chain340] [gw1] [ 70%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain316-method_chain316] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain317-method_chain317] [gw3] [ 70%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain326-method_chain326] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain327-method_chain327] [gw4] [ 70%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain227-method_chain227] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain228-method_chain228] [gw5] [ 70%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain340-method_chain340] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain341-method_chain341] [gw7] [ 70%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain237-method_chain237] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain336-method_chain336] [gw4] [ 71%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain228-method_chain228] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain352-method_chain352] [gw6] [ 71%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain306-method_chain306] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain307-method_chain307] [gw9] [ 71%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain313-method_chain313] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain314-method_chain314] [gw9] [ 71%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain314-method_chain314] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain315-method_chain315] [gw0] [ 71%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain322-method_chain322] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain323-method_chain323] [gw10] [ 72%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain284-method_chain284] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain348-method_chain348] [gw4] [ 72%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain352-method_chain352] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain353-method_chain353] [gw3] [ 72%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain327-method_chain327] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain328-method_chain328] [gw6] [ 72%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain307-method_chain307] [gw5] [ 72%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain341-method_chain341] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain308-method_chain308] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain342-method_chain342] [gw3] [ 73%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain328-method_chain328] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain329-method_chain329] [gw5] [ 73%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain342-method_chain342] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain343-method_chain343] [gw8] [ 73%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain332-method_chain332] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain333-method_chain333] [gw2] [ 73%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain344-method_chain344] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain345-method_chain345] [gw1] [ 73%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain317-method_chain317] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain318-method_chain318] [gw7] [ 74%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain336-method_chain336] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain337-method_chain337] [gw4] [ 74%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain353-method_chain353] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain354-method_chain354] [gw0] [ 74%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain323-method_chain323] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain324-method_chain324] [gw10] [ 74%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain348-method_chain348] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain349-method_chain349] [gw2] [ 74%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain345-method_chain345] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain346-method_chain346] [gw6] [ 74%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain308-method_chain308] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain309-method_chain309] [gw0] [ 75%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain324-method_chain324] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain325-method_chain325] [gw5] [ 75%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain343-method_chain343] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain360-method_chain360] [gw9] [ 75%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain315-method_chain315] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain356-method_chain356] [gw8] [ 75%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain333-method_chain333] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain334-method_chain334] [gw7] [ 75%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain337-method_chain337] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain338-method_chain338] [gw4] [ 76%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain354-method_chain354] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain355-method_chain355] [gw1] [ 76%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain318-method_chain318] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain319-method_chain319] [gw7] [ 76%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain338-method_chain338] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain339-method_chain339] [gw2] [ 76%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain346-method_chain346] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain347-method_chain347] [gw3] [ 76%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain329-method_chain329] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain330-method_chain330] [gw10] [ 77%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain349-method_chain349] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain350-method_chain350] [gw8] [ 77%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain334-method_chain334] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain335-method_chain335] [gw9] [ 77%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain356-method_chain356] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain357-method_chain357] [gw6] [ 77%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain309-method_chain309] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain363-method_chain363] [gw6] [ 77%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain363-method_chain363] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain364-method_chain364] [gw2] [ 77%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain347-method_chain347] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain375-method_chain375] [gw2] [ 78%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain375-method_chain375] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain376-method_chain376] [gw0] [ 78%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain325-method_chain325] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain366-method_chain366] [gw4] [ 78%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain355-method_chain355] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain369-method_chain369] [gw10] [ 78%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain350-method_chain350] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain351-method_chain351] [gw8] [ 78%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain335-method_chain335] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain381-method_chain381] [gw5] [ 79%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain360-method_chain360] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain361-method_chain361] [gw1] [ 79%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain319-method_chain319] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain320-method_chain320] [gw5] [ 79%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain361-method_chain361] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain362-method_chain362] [gw9] [ 79%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain357-method_chain357] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain358-method_chain358] [gw3] [ 79%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain330-method_chain330] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain378-method_chain378] [gw7] [ 80%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain339-method_chain339] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain372-method_chain372] [gw2] [ 80%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain376-method_chain376] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain377-method_chain377] [gw2] [ 80%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain377-method_chain377] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain389-method_chain389] [gw2] [ 80%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain389-method_chain389] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain390-method_chain390] [gw6] [ 80%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain364-method_chain364] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain365-method_chain365] [gw5] [ 80%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain362-method_chain362] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain387-method_chain387] [gw5] [ 81%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain387-method_chain387] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain388-method_chain388] [gw10] [ 81%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain351-method_chain351] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain383-method_chain383] [gw9] [ 81%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain358-method_chain358] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain359-method_chain359] [gw0] [ 81%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain366-method_chain366] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain367-method_chain367] [gw7] [ 81%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain372-method_chain372] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain373-method_chain373] [gw9] [ 82%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain359-method_chain359] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain397-method_chain397] [gw4] [ 82%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain369-method_chain369] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain370-method_chain370] [gw7] [ 82%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain373-method_chain373] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain374-method_chain374] [gw2] [ 82%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain390-method_chain390] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain391-method_chain391] [gw2] [ 82%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain391-method_chain391] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain392-method_chain392] [gw3] [ 83%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain378-method_chain378] [gw8] [ 83%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain381-method_chain381] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain379-method_chain379] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain382-method_chain382] [gw1] [ 83%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain320-method_chain320] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain385-method_chain385] [gw10] [ 83%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain383-method_chain383] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain384-method_chain384] [gw5] [ 83%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain388-method_chain388] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain395-method_chain395] [gw9] [ 83%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain397-method_chain397] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain398-method_chain398] [gw8] [ 84%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain382-method_chain382] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain402-method_chain402] [gw6] [ 84%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain365-method_chain365] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain393-method_chain393] [gw1] [ 84%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain385-method_chain385] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain386-method_chain386] [gw4] [ 84%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain370-method_chain370] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain371-method_chain371] [gw2] [ 84%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain392-method_chain392] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain401-method_chain401] [gw0] [ 85%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain367-method_chain367] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain368-method_chain368] [gw3] [ 85%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain379-method_chain379] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain380-method_chain380] [gw7] [ 85%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain374-method_chain374] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain399-method_chain399] [gw10] [ 85%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain384-method_chain384] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain403-method_chain403] [gw8] [ 85%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain402-method_chain402] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain405-method_chain405] [gw9] [ 86%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain398-method_chain398] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain404-method_chain404] [gw5] [ 86%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain395-method_chain395] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain396-method_chain396] [gw2] [ 86%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain401-method_chain401] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain408-method_chain408] [gw10] [ 86%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain403-method_chain403] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain411-method_chain411] [gw2] [ 86%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain408-method_chain408] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain415-method_chain415] [gw1] [ 87%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain386-method_chain386] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain406-method_chain406] [gw6] [ 87%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain393-method_chain393] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain394-method_chain394] [gw4] [ 87%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain371-method_chain371] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain407-method_chain407] [gw8] [ 87%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain405-method_chain405] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain412-method_chain412] [gw3] [ 87%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain380-method_chain380] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain410-method_chain410] [gw5] [ 87%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain396-method_chain396] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain414-method_chain414] [gw7] [ 88%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain399-method_chain399] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain400-method_chain400] [gw8] [ 88%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain412-method_chain412] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain421-method_chain421] [gw3] [ 88%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain410-method_chain410] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain422-method_chain422] [gw0] [ 88%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain368-method_chain368] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain409-method_chain409] [gw3] [ 88%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain422-method_chain422] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain426-method_chain426] [gw0] [ 89%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain409-method_chain409] [gw9] [ 89%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain404-method_chain404] [gw3] [ 89%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain426-method_chain426] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain427-method_chain427] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain428-method_chain428] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain413-method_chain413] [gw10] [ 89%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain411-method_chain411] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain416-method_chain416] [gw6] [ 89%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain394-method_chain394] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain419-method_chain419] [gw4] [ 90%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain407-method_chain407] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain420-method_chain420] [gw1] [ 90%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain406-method_chain406] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain418-method_chain418] [gw8] [ 90%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain421-method_chain421] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain425-method_chain425] [gw7] [ 90%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain400-method_chain400] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain424-method_chain424] [gw2] [ 90%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain415-method_chain415] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain417-method_chain417] [gw7] [ 90%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain424-method_chain424] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain437-method_chain437] [gw7] [ 91%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain437-method_chain437] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain439-method_chain439] [gw5] [ 91%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain414-method_chain414] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain423-method_chain423] [gw3] [ 91%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain428-method_chain428] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain430-method_chain430] [gw5] [ 91%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain423-method_chain423] tests/test_genomicfeatures.py::test_introns_single [gw5] [ 91%] FAILED tests/test_genomicfeatures.py::test_introns_single tests/test_getset_attr.py::test_getsetattr_fails [gw5] [ 92%] PASSED tests/test_getset_attr.py::test_getsetattr_fails tests/test_getset_attr.py::test_getsetattr_with_str [gw5] [ 92%] PASSED tests/test_getset_attr.py::test_getsetattr_with_str tests/test_io.py::test_read_gtf [gw5] [ 92%] PASSED tests/test_io.py::test_read_gtf tests/test_io.py::test_read_gff3 [gw5] [ 92%] PASSED tests/test_io.py::test_read_gff3 tests/test_io.py::test_read_bed [gw5] [ 92%] PASSED tests/test_io.py::test_read_bed tests/test_pickle.py::test_pickle [gw5] [ 93%] PASSED tests/test_pickle.py::test_pickle tests/test_stranded.py::test_stranded [gw5] [ 93%] PASSED tests/test_stranded.py::test_stranded tests/test_stranded.py::test_unstrand [gw5] [ 93%] PASSED tests/test_stranded.py::test_unstrand tests/test_unary.py::test_merge[True] [gw0] [ 93%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain427-method_chain427] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain429-method_chain429] [gw9] [ 93%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain413-method_chain413] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain431-method_chain431] [gw8] [ 93%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain425-method_chain425] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain436-method_chain436] [gw4] [ 94%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain420-method_chain420] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain434-method_chain434] [gw5] [ 94%] FAILED tests/test_unary.py::test_merge[True] tests/test_unary.py::test_merge[False] [gw8] [ 94%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain436-method_chain436] tests/test_unary.py::test_cluster_by[True] [gw10] [ 94%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain416-method_chain416] [gw6] [ 94%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain419-method_chain419] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain432-method_chain432] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain433-method_chain433] [gw5] [ 95%] FAILED tests/test_unary.py::test_merge[False] tests/test_unary.py::test_merge_by[True] [gw7] [ 95%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain439-method_chain439] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain440-method_chain440] [gw1] [ 95%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain418-method_chain418] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain435-method_chain435] [gw7] [ 95%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain440-method_chain440] tests/test_unary.py::test_getitem [gw0] [ 95%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain429-method_chain429] tests/test_unary.py::test_cluster[True] [gw2] [ 96%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain417-method_chain417] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain438-method_chain438] [gw4] [ 96%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain434-method_chain434] tests/test_unary.py::test_cluster_by[False] [gw2] [ 96%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain438-method_chain438] [gw6] [ 96%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain433-method_chain433] tests/test_unary.py::test_init[True] [gw10] [ 96%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain432-method_chain432] tests/test_unary.py::test_windows [gw9] [ 96%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain431-method_chain431] tests/test_unary.py::test_cluster[False] [gw7] [ 97%] PASSED tests/test_unary.py::test_getitem tests/windows/test_windows.py::test_windows [gw7] [ 97%] FAILED tests/windows/test_windows.py::test_windows [gw3] [ 97%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain430-method_chain430] tests/test_getset_attr.py::test_getsetattr [gw3] [ 97%] PASSED tests/test_getset_attr.py::test_getsetattr [gw0] [ 97%] FAILED tests/test_unary.py::test_cluster[True] tests/windows/test_windows.py::test_windows2 [gw0] [ 98%] FAILED tests/windows/test_windows.py::test_windows2 [gw6] [ 98%] PASSED tests/test_unary.py::test_init[True] [gw10] [ 98%] FAILED tests/test_unary.py::test_windows [gw1] [ 98%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain435-method_chain435] tests/test_unary.py::test_summary [gw9] [ 98%] FAILED tests/test_unary.py::test_cluster[False] [gw1] [ 99%] FAILED tests/test_unary.py::test_summary [gw5] [ 99%] PASSED tests/test_unary.py::test_merge_by[True] tests/test_unary.py::test_init[False] [gw5] [ 99%] PASSED tests/test_unary.py::test_init[False] [gw8] [ 99%] PASSED tests/test_unary.py::test_cluster_by[True] tests/test_unary.py::test_merge_by[False] [gw4] [ 99%] PASSED tests/test_unary.py::test_cluster_by[False] [gw8] [100%] PASSED tests/test_unary.py::test_merge_by[False] =================================== FAILURES =================================== ___________________ test_k_nearest[upstream-False-same-last] ___________________ [gw4] linux -- Python 3.12.6 /usr/bin/python3.12 nearest_how = 'upstream', overlap = False, strandedness = 'same', ties = 'last' @pytest.mark.bedtools > @pytest.mark.explore tests/test_binary.py:510: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:548: in test_k_nearest result = gr.k_nearest( pyranges/pyranges.py:2450: in k_nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/k_nearest.py:180: in _nearest df = __nearest(d1, d2, **kwargs) pyranges/methods/k_nearest.py:115: in nearest_previous lidx, ridx, dist = nearest_previous_idx(d1, d2, d1.__k__.values, ties) pyranges/methods/k_nearest.py:28: in nearest_previous_idx lidx, ridx_pos, dist = k_nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_k_nearest( E nearest_how='upstream', E overlap=False, E strandedness='same', E ties='last', E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:14 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:15 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:160 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:171 E (and 40 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2TABIxYxAAAZAAD') as a decorator on your test case sorted_nearest/src/k_nearest.pyx:28: ValueError ----------------------------- Captured stdout call ----------------------------- ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7v2nh0o_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7v2nh0o_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6cqhowat/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6cqhowat/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpe4vn3tb4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe4vn3tb4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8jlgvrr9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8jlgvrr9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp07hhnili/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp07hhnili/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmppxjfaevr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppxjfaevr/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyqfiexj4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyqfiexj4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2ey450h2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2ey450h2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpt73qtxmy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt73qtxmy/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp54uklbiv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp54uklbiv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp37y6vevi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp37y6vevi/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpf9htsu8a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf9htsu8a/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwdvvmp6i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwdvvmp6i/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpr1h6zwjr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr1h6zwjr/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_y9c7vil/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_y9c7vil/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdbqzczwd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdbqzczwd/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4fm8t39s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4fm8t39s/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp89vx8eij/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp89vx8eij/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpp2o2qq8s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp2o2qq8s/f2.bed) ----------------------------- Captured stderr call ----------------------------- Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. ___________ test_three_in_a_row[strandedness_chain55-method_chain55] ___________ [gw9] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', 'same'), method_chain = ('set_union', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('set_union', 'join'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E (and 177 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2AUZ5lkUCgkw8DIgAUAACbgAX8=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') __________________ test_k_nearest[upstream-False-False-last] ___________________ [gw4] linux -- Python 3.12.6 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 880, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 510, in test_k_nearest | @pytest.mark.explore | ^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1722, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 548, in test_k_nearest | result = gr.k_nearest( | ^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2450, in k_nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 292, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 180, in _nearest | df = __nearest(d1, d2, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 140, in nearest_next | lidx, ridx, dist = nearest_next_idx(d1, d2, d1.__k__.values, ties) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 56, in nearest_next_idx | lidx, ridx_pos, dist = k_nearest_next_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/k_nearest.pyx", line 55, in sorted_nearest.src.k_nearest.k_nearest_next_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_k_nearest( | nearest_how='upstream', | overlap=False, | strandedness=False, | ties='last', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:160 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:171 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:41 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:42 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:46 | (and 38 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2TAAIyMmGIMAAB5AAQ=') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 548, in test_k_nearest | result = gr.k_nearest( | ^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2450, in k_nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 292, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 180, in _nearest | df = __nearest(d1, d2, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 115, in nearest_previous | lidx, ridx, dist = nearest_previous_idx(d1, d2, d1.__k__.values, ties) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 28, in nearest_previous_idx | lidx, ridx_pos, dist = k_nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/k_nearest.pyx", line 28, in sorted_nearest.src.k_nearest.k_nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_k_nearest( | nearest_how='upstream', | overlap=False, | strandedness=False, | ties='last', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:14 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:15 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:160 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:171 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:19 | (and 38 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2TABIxYxAAAZAAD') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3_2z4izg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3_2z4izg/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxpc83uv2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxpc83uv2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzj2tqxr5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzj2tqxr5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpw_xpdc3p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw_xpdc3p/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpo38zgvl3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo38zgvl3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpob5qdce5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpob5qdce5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpt_3wgn3b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt_3wgn3b/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7x53rgxl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7x53rgxl/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzz7vdwrr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzz7vdwrr/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp04o1gunl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp04o1gunl/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmplqnos_qi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplqnos_qi/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqn1ih0vx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqn1ih0vx/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnp0xieae/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnp0xieae/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpp5ypduiv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp5ypduiv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbc4ycisl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbc4ycisl/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_qj_vxf_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_qj_vxf_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7dyzfnl5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7dyzfnl5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqu1xumhz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqu1xumhz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpc3pmwmgu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc3pmwmgu/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgiib2ttz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgiib2ttz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9mpzmuox/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9mpzmuox/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpea5tyxpc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpea5tyxpc/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp74qrg6i7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp74qrg6i7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmphhgl_p85/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphhgl_p85/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_tgq28fl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_tgq28fl/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmlkv5o66/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmlkv5o66/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpf4zkpf5i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf4zkpf5i/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzr6a_451/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzr6a_451/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0p4e3xkd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0p4e3xkd/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0fcw5_75/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0fcw5_75/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbylg_wbx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbylg_wbx/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmptnccw7x6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptnccw7x6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpv61nq5iw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv61nq5iw/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmpsr2dul/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmpsr2dul/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4ig7dpeu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4ig7dpeu/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpl_dorfv8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl_dorfv8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvz4nav_x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvz4nav_x/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpk18zu_kj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk18zu_kj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp77fq9enf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp77fq9enf/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3439h7fa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3439h7fa/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqs_0enbn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqs_0enbn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpndgz4a9h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpndgz4a9h/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_7znbrgd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_7znbrgd/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmplvj6rzgo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplvj6rzgo/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp587zwrj0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp587zwrj0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmparnt610a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmparnt610a/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp493nu6e_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp493nu6e_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_4rc546f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_4rc546f/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7ejhtbhp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7ejhtbhp/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmptxrtbs6y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptxrtbs6y/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnou952q9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnou952q9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdg37yy9b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdg37yy9b/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpi4d_j5l_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi4d_j5l_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnqihw53q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnqihw53q/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpi19yyot7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi19yyot7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpo6zqiwtf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo6zqiwtf/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmppek4764e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppek4764e/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4rvdioib/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4rvdioib/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqnqfi3zz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqnqfi3zz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpd6cdahh6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd6cdahh6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmprospo9kg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprospo9kg/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5bz4w3x2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5bz4w3x2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpien4edn1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpien4edn1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_dl9cbfu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_dl9cbfu/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8qed9s4x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8qed9s4x/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3mu243at/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3mu243at/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpz7_g5v7d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz7_g5v7d/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpya9cbwpq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpya9cbwpq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpn8p83emd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn8p83emd/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4hdwh4kc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4hdwh4kc/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpz0y6ekom/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz0y6ekom/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfyvuleew/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfyvuleew/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpi1ox_b8_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi1ox_b8_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcgay1bec/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcgay1bec/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmptv2rb433/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptv2rb433/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpl1mmycva/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl1mmycva/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1w8v6plu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1w8v6plu/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0o6qzc8n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0o6qzc8n/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpr5r38pd9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr5r38pd9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp54zskg0e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp54zskg0e/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfeyytsgd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfeyytsgd/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuhnv8li8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuhnv8li8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5fpnusez/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5fpnusez/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpf3t1yblx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf3t1yblx/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnbd156gn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnbd156gn/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpckib_4ll/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpckib_4ll/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8jvw8g4k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8jvw8g4k/f2.bed) ----------------------------- Captured stderr call ----------------------------- Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. ___________ test_three_in_a_row[strandedness_chain19-method_chain19] ___________ [gw6] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', False), method_chain = ('overlap', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('overlap', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:15 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:145 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:369 E (and 23 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BAAEYUCgwAAD4AAw==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ___________ test_three_in_a_row[strandedness_chain43-method_chain43] ___________ [gw10] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', False), method_chain = ('join', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('join', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:38 E (and 160 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ____________ test_three_in_a_row[strandedness_chain7-method_chain7] ____________ [gw7] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', False) method_chain = ('set_intersect', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('set_intersect', 'set_union'), E gr=Empty PyRanges, # or any other generated value E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:117 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E (and 125 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BAAEYGTAAAADQAAg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ____________ test_three_in_a_row[strandedness_chain0-method_chain0] ____________ [gw5] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', False), method_chain = ('set_union', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('set_union', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E (and 250 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2DMiXQIdRBYwsjAyIAJADw9AlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ______________________________ test_jaccard[same] ______________________________ [gw3] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness = 'same' @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness", no_opposite) tests/test_binary.py:363: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:378: in test_jaccard result = gr.stats.jaccard(gr2, strandedness=strandedness) pyranges/statistics.py:766: in jaccard for v in self.set_intersect(other).lengths(as_dict=True).values()) pyranges/pyranges.py:3687: in set_intersect self_clusters = self.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_jaccard( E # The test always failed when commented parts were varied together. E strandedness='same', E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., # or any other generated value E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., # or any other generated value E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2TABIxYxAAAZAAD') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception _______________________ test_nearest[upstream-True-same] _______________________ [gw2] linux -- Python 3.12.6 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 880, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 323, in test_nearest | @pytest.mark.parametrize("nearest_how,overlap,strandedness", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1722, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 3 distinct failures. (3 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 351, in test_nearest | result = gr.nearest( | ^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 115, in _nearest | r_idx, dist = _next_nonoverlapping(df_to_find_nearest_in.End, | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 62, in _next_nonoverlapping | r_idx, dist = nearest_next_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 34, in sorted_nearest.src.sorted_nearest.nearest_next_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_nearest( | nearest_how='upstream', | overlap=True, | strandedness='same', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | (and 124 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2QAA0YGOGBkRKZhHAAAwAAJ') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 351, in test_nearest | result = gr.nearest( | ^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 118, in _nearest | r_idx, dist = _previous_nonoverlapping(df_to_find_nearest_in.Start, | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_nearest( | nearest_how='upstream', | overlap=True, | strandedness='same', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | (and 125 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2QAA0YGBGCEkozIMgAAqQAH') as a decorator on your test case +---------------- 3 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 359, in test_nearest | compare_results_nearest(bedtools_df, result) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 107, in compare_results_nearest | assert_df_equal(result_df, bedtools_df) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/helpers.py", line 60, in assert_df_equal | pd.testing.assert_frame_equal(df1, df2) | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 1279, in assert_frame_equal | assert_series_equal( | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 975, in assert_series_equal | assert_attr_equal("dtype", left, right, obj=f"Attributes of {obj}") | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 421, in assert_attr_equal | raise_assert_detail(obj, msg, left_attr, right_attr) | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 614, in raise_assert_detail | raise AssertionError(msg) | AssertionError: Attributes of DataFrame.iloc[:, 4] (column name="Distance") are different | | Attribute "dtype" are different | [left]: int32 | [right]: int64 | Falsifying example: test_nearest( | nearest_how='upstream', | overlap=True, | strandedness='same', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | (and 457 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpr6gwmlfh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr6gwmlfh/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5ifdyf53/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5ifdyf53/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp51qunrh2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp51qunrh2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmmmef14o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmmmef14o/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_ulv95ia/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_ulv95ia/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjliqarh2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjliqarh2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpc4d1m8e8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc4d1m8e8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmph4o60fil/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph4o60fil/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe7u97zky/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe7u97zky/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzbsv5n8p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzbsv5n8p/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfywlreq_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfywlreq_/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpv7wi_90h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv7wi_90h/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9jqmkjjc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9jqmkjjc/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbcf0kjkc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbcf0kjkc/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyt2xlqdp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyt2xlqdp/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzy07aym1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzy07aym1/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpo60lwtl5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo60lwtl5/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjwhmq1z8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjwhmq1z8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2nng825_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2nng825_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpv2x0ordr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv2x0ordr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpobzuh04o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpobzuh04o/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_1kqnhg3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_1kqnhg3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgjnjg06_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgjnjg06_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzs8dwzz3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzs8dwzz3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpt7k8fb9k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt7k8fb9k/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpijpaviqu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpijpaviqu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe1vkwuyk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe1vkwuyk/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpra8y69f5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpra8y69f5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp740r5368/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp740r5368/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprmh1kt8a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprmh1kt8a/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8_q4raff/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8_q4raff/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppbddl34s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppbddl34s/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqy4doqj6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqy4doqj6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjjd0hxpn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjjd0hxpn/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprch1kp7y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprch1kp7y/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcf5pcn7s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcf5pcn7s/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxz06cbwt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxz06cbwt/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpc03zrzlc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc03zrzlc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6xagvu19/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6xagvu19/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpx9hya4f6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx9hya4f6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7tros6wz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7tros6wz/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwjx_3s5a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwjx_3s5a/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprc47f75n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprc47f75n/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpu45y91x_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu45y91x_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpy6j8dnih/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy6j8dnih/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpr1uljbfd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr1uljbfd/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmps81zyjby/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps81zyjby/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpki8ypjmy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpki8ypjmy/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfuhlf2li/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfuhlf2li/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdlhsrnqh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdlhsrnqh/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7tjo2yd2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7tjo2yd2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfzc98i8b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfzc98i8b/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_a4cu3ki/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_a4cu3ki/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkcprpyp5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkcprpyp5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqd_yeyz_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqd_yeyz_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8jt9tclz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8jt9tclz/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcl02wmuf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcl02wmuf/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0dhf2ruo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0dhf2ruo/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpr2s3wzt5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr2s3wzt5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp36_covf0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp36_covf0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpm0ac7epw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm0ac7epw/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqezg2du8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqezg2du8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe37h3zdb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe37h3zdb/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxid8p0yw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxid8p0yw/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmps0d7_9aw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps0d7_9aw/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9g7p9v11/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9g7p9v11/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvkbuzfv8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvkbuzfv8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxayghomc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxayghomc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7p70c35g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7p70c35g/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsi6zgssa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsi6zgssa/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvr5be1a9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvr5be1a9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzik0m6nh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzik0m6nh/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp71n72v07/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp71n72v07/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuu9disi7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuu9disi7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdsf_ilc1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdsf_ilc1/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpaao548ko/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaao548ko/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvwb_6ryk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvwb_6ryk/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqs41saay/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqs41saay/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp23cxh9o3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp23cxh9o3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsuj1ymzm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsuj1ymzm/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpn4ns98f3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn4ns98f3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpb3zq8nfm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb3zq8nfm/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppk9juarq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppk9juarq/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqaxetynv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqaxetynv/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwmf5fjyo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwmf5fjyo/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe8psu1bb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe8psu1bb/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1zc91fse/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1zc91fse/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpj_s4e8k3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj_s4e8k3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprup2ef0b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprup2ef0b/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp54k_ivaa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp54k_ivaa/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppc3e0w2g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppc3e0w2g/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpu3yzv2r3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu3yzv2r3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4h35n8cn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4h35n8cn/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpo4sdguzk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo4sdguzk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpj5qoixaj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj5qoixaj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1hvpa2qo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1hvpa2qo/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvygiud15/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvygiud15/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3arrlwy_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3arrlwy_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpd7m1md6b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd7m1md6b/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4791etx7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4791etx7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxgha15ku/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxgha15ku/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3srnm_mo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3srnm_mo/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwe54pz2_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwe54pz2_/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpb0kq9m1d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb0kq9m1d/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxuzm4vd3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxuzm4vd3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpleji5ipo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpleji5ipo/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnlsparpe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnlsparpe/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpib3lokf9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpib3lokf9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_lnntxh3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_lnntxh3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkiauyn3f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkiauyn3f/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzbl2okyu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzbl2okyu/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqtmzlc91/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqtmzlc91/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1h38gfta/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1h38gfta/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1nggajp9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1nggajp9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpu0ct6yd9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu0ct6yd9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyqz_nmws/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyqz_nmws/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpt4f_8trs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt4f_8trs/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxob14i1z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxob14i1z/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpd79fppr1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd79fppr1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpeg7xkt_b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpeg7xkt_b/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpv7w17tud/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv7w17tud/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpctnm2r02/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpctnm2r02/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmph2kyjuhy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph2kyjuhy/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqmnmeo9w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqmnmeo9w/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfmkbjuw5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfmkbjuw5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkx2094rc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkx2094rc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1v8y8znm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1v8y8znm/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdc8skyi_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdc8skyi_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpy8jpd6d8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy8jpd6d8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp12r7nfa8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp12r7nfa8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcioc6_bb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcioc6_bb/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp59adn76u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp59adn76u/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmwtas78b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmwtas78b/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5sq7pxmh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5sq7pxmh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpn96pej8x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn96pej8x/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpixag8ucw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpixag8ucw/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpow4sbljy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpow4sbljy/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplxhkl2_v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplxhkl2_v/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpycbnf9td/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpycbnf9td/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6kol8vjl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6kol8vjl/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp84ngw817/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp84ngw817/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjml3gekk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjml3gekk/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjgerga4s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjgerga4s/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3g77kzep/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3g77kzep/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxt429kcn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxt429kcn/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdjbdo5rb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdjbdo5rb/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcsfzngol/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcsfzngol/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnwvor9d3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnwvor9d3/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmo2at6bb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmo2at6bb/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvkmrm0ol/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvkmrm0ol/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp72_ul4ks/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp72_ul4ks/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpj64rvbw8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj64rvbw8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvc2y5qja/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvc2y5qja/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpabu75oq6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpabu75oq6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp87u02ioh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp87u02ioh/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpq9xyu2o3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq9xyu2o3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmh14rwr6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmh14rwr6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6h8eczrb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6h8eczrb/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqrktg55y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqrktg55y/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwskz5o47/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwskz5o47/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpj20v1yz7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj20v1yz7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdxke8jx6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdxke8jx6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpk0ob40nt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk0ob40nt/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprt8n_sd_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprt8n_sd_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9nd4ijmz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9nd4ijmz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpy1m1y3ik/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy1m1y3ik/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptubgo5d1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptubgo5d1/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprl1idrh7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprl1idrh7/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp48x90z6q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp48x90z6q/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpeln64kgt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpeln64kgt/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpx5k3odl9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx5k3odl9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpw9cgctvu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw9cgctvu/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmps2i0ch1h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps2i0ch1h/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpg_oz9zkm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg_oz9zkm/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmph0bp9gna/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph0bp9gna/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkmo2czi2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkmo2czi2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcjnj1gxx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcjnj1gxx/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2jug_9ai/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2jug_9ai/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1k8eorjn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1k8eorjn/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp84f0ch_x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp84f0ch_x/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpww1wsljz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpww1wsljz/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0hwz0po3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0hwz0po3/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpht0vdo81/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpht0vdo81/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptewjydo3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptewjydo3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpu6r8dhuh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu6r8dhuh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpstocazjk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpstocazjk/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmyao4bmj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmyao4bmj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppnraqc7e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppnraqc7e/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9zw8q2qa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9zw8q2qa/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5mk35ljq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5mk35ljq/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppe068mps/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppe068mps/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplnsnfwi8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplnsnfwi8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplq_couns/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplq_couns/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpipdl6inq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpipdl6inq/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbyxc0j3y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbyxc0j3y/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5qgo86zv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5qgo86zv/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpd5cbmbry/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd5cbmbry/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqwdhypky/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqwdhypky/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuxxl4lqx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuxxl4lqx/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjb2s0pde/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjb2s0pde/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5d9jc6oj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5d9jc6oj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppeo2qmj1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppeo2qmj1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppdr7rx7x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppdr7rx7x/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsq8o213_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsq8o213_/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________________________ test_set_intersect[False] ___________________________ [gw0] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness = False @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness", no_opposite) tests/test_binary.py:113: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:128: in test_set_intersect result = gr.set_intersect(gr2, strandedness=strandedness) pyranges/pyranges.py:3687: in set_intersect self_clusters = self.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_set_intersect( E strandedness=False, E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., # or any other generated value E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., # or any other generated value E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2TABIxYxAAAZAAD') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp96dqg5qe/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp96dqg5qe/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmph3qpt_b4/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmph3qpt_b4/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpaog9ho65/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpaog9ho65/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpcsfs64ls/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpcsfs64ls/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp0_ijbpr0/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp0_ijbpr0/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpndvwv4po/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpndvwv4po/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp5a0f9f4m/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp5a0f9f4m/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpp48tghgw/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpp48tghgw/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpisayjpjb/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpisayjpjb/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpk596j5sk/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpk596j5sk/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmprpnfdzcw/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmprpnfdzcw/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpd9b3tvly/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpd9b3tvly/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp8kea0_zp/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp8kea0_zp/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpoi7y79_5/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpoi7y79_5/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpkqpe9bzt/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpkqpe9bzt/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpuvgza1jn/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpuvgza1jn/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp29en5jo9/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp29en5jo9/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp0d0el8vc/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp0d0el8vc/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpyh9g1myz/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpyh9g1myz/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpa8zr6m75/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpa8zr6m75/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp7qai9zm1/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp7qai9zm1/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp4p1692u3/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp4p1692u3/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpad6154sq/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpad6154sq/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpdr1vywxb/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpdr1vywxb/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpel4agsvl/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpel4agsvl/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp7asti7_q/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp7asti7_q/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp9rkwhy18/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp9rkwhy18/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmphkq_xk29/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmphkq_xk29/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpf805wpah/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpf805wpah/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp9el7tnj2/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp9el7tnj2/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpqcigaqpa/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpqcigaqpa/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpdxccs6l7/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpdxccs6l7/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp1j8ur8ur/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp1j8ur8ur/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpzv5lm80l/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpzv5lm80l/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpu5ga13sn/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpu5ga13sn/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpr1_e931s/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpr1_e931s/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpd20zdgqa/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpd20zdgqa/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp1qzfz5pl/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp1qzfz5pl/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmplg85lalf/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmplg85lalf/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpell_rmr_/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpell_rmr_/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp9u587k5z/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp9u587k5z/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp7i2gpco5/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp7i2gpco5/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpp0cyw250/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpp0cyw250/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp5l6bsec4/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp5l6bsec4/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpgoz_piug/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpgoz_piug/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp78n3yydh/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp78n3yydh/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp2o8z57qg/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp2o8z57qg/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpp3glqp7y/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpp3glqp7y/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmps1ru9zxi/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmps1ru9zxi/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpnvr01cev/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpnvr01cev/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp2vrgo2hq/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp2vrgo2hq/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpphg9bd7j/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpphg9bd7j/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpjgmzjdy5/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpjgmzjdy5/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp88a05w3l/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp88a05w3l/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpo5t4x51j/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpo5t4x51j/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmppp50s14d/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmppp50s14d/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpzioldlew/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpzioldlew/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp999e9nio/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp999e9nio/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp8ck581xy/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp8ck581xy/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp6zhlk5cs/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp6zhlk5cs/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp5zq75po6/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp5zq75po6/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp8wl7sf80/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp8wl7sf80/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp1s0tv_7w/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp1s0tv_7w/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpcde314z7/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpcde314z7/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmprqicdokx/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmprqicdokx/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmprr9h1bl3/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmprr9h1bl3/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpj_rdu8lk/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpj_rdu8lk/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp4h7yk7rt/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp4h7yk7rt/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpz_bhcvdu/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpz_bhcvdu/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpk65r0juj/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpk65r0juj/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmptjvtdit1/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmptjvtdit1/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmphm3qcng6/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmphm3qcng6/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpc596vbdv/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpc596vbdv/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpxoo8v1el/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpxoo8v1el/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpu2kxk6bo/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpu2kxk6bo/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpaaevsp7u/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpaaevsp7u/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpbc0h8iif/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpbc0h8iif/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpdw4ptzcy/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpdw4ptzcy/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp64ire8ey/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp64ire8ey/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmptzfmx6ta/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmptzfmx6ta/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpm95c_15h/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpm95c_15h/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp2v5no28r/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp2v5no28r/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpl6m0dmwu/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpl6m0dmwu/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmptg9gp8lm/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmptg9gp8lm/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpy19nmkpa/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpy19nmkpa/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpmo6nnvrv/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpmo6nnvrv/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpe1kn1sod/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpe1kn1sod/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmps9hgvgi5/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmps9hgvgi5/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpjotm7vfm/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpjotm7vfm/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpo4f_d1pt/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpo4f_d1pt/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpqsizr666/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpqsizr666/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpgff804nh/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpgff804nh/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpmizgdeu_/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpmizgdeu_/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpdq5bvgga/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpdq5bvgga/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpumuwfy4s/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpumuwfy4s/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp2nmwzff1/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp2nmwzff1/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp4ja870qr/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp4ja870qr/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpg3vq1_jy/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpg3vq1_jy/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpijelecj1/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpijelecj1/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp4hm32yd0/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp4hm32yd0/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpqg164wfi/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpqg164wfi/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpt3_bhyel/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpt3_bhyel/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpvz6qvnuo/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpvz6qvnuo/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp5ad_m4dm/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp5ad_m4dm/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp2ry9051n/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp2ry9051n/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpslcpchvs/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpslcpchvs/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpmgwuzgbk/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpmgwuzgbk/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpintmcc_1/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpintmcc_1/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpyh9vw2xu/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpyh9vw2xu/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp292v1aeh/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp292v1aeh/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpgnoyukh1/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpgnoyukh1/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpmmembov3/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpmmembov3/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp7352fkip/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp7352fkip/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpzc1wyw47/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpzc1wyw47/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp39coxf61/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp39coxf61/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp3uhle73f/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp3uhle73f/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp6p97obeu/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp6p97obeu/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpcmb3b991/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpcmb3b991/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpw2z7z1dh/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpw2z7z1dh/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpu4r47oyq/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpu4r47oyq/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpttmuf4lu/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpttmuf4lu/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpo_8x_rfm/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpo_8x_rfm/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpkqxi_q8s/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpkqxi_q8s/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpk3x9r2w2/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpk3x9r2w2/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp6e1li1ev/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp6e1li1ev/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmprbp74a4m/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmprbp74a4m/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp0m5wr1h5/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp0m5wr1h5/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpyy3pb59y/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpyy3pb59y/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpv3_69dj6/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpv3_69dj6/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp0f26sqpa/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp0f26sqpa/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpcbm_pep8/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpcbm_pep8/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpppgcizd9/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpppgcizd9/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpgog7jdlq/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpgog7jdlq/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp94kz4ma3/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp94kz4ma3/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpyud7kpqt/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpyud7kpqt/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpl1gtiz5o/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpl1gtiz5o/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpqpku4jby/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpqpku4jby/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpy0581q4x/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpy0581q4x/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpeksrbnck/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpeksrbnck/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp4s9ldi9v/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp4s9ldi9v/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmps2s2bv3n/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmps2s2bv3n/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpjjfo9qmk/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpjjfo9qmk/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp2crb1wo9/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp2crb1wo9/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpctlwpj7g/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpctlwpj7g/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpwd_nwa47/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpwd_nwa47/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp4vlop57e/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp4vlop57e/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpx07xwfaz/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpx07xwfaz/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp26svkmho/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp26svkmho/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp8zwevow0/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp8zwevow0/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp8pq_9bgm/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp8pq_9bgm/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpk6fetegh/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpk6fetegh/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmphhnjhd9o/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmphhnjhd9o/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmphajyxtsq/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmphajyxtsq/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp_228h7uh/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp_228h7uh/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpjrlqenbm/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpjrlqenbm/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp3mtiz_et/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp3mtiz_et/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpjtmql48u/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpjtmql48u/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpjo83quz6/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpjo83quz6/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpagwfwuzb/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpagwfwuzb/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpxxbqzpqp/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpxxbqzpqp/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpat8le_oe/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpat8le_oe/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpf2r9kjza/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpf2r9kjza/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpoxspi2qo/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpoxspi2qo/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpp5wlz80k/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpp5wlz80k/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp5fjjqh_m/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp5fjjqh_m/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpceruef_i/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpceruef_i/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpmooq09oj/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpmooq09oj/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpin65_s81/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpin65_s81/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp5c83fjsl/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp5c83fjsl/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpzt01xqyo/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpzt01xqyo/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpdm8cr5hi/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpdm8cr5hi/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpzcw5qi04/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpzcw5qi04/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpc3nnhphh/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpc3nnhphh/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp_3os7osd/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp_3os7osd/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpv7_idcx6/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpv7_idcx6/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpy9ylxvtf/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpy9ylxvtf/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpo1pgcvgt/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpo1pgcvgt/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpdrv5_f80/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpdrv5_f80/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmphz2lows0/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmphz2lows0/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpxcb23iu1/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpxcb23iu1/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmphs0tddb1/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmphs0tddb1/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpkh5ikggj/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpkh5ikggj/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp1h9nkxa1/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp1h9nkxa1/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp0_1lw5mj/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp0_1lw5mj/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpdrhv9x9a/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpdrhv9x9a/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpqpqj_nq5/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpqpqj_nq5/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpkackdwnj/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpkackdwnj/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmppwdu0btr/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmppwdu0btr/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp59i9uj41/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp59i9uj41/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpq6an7j0y/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpq6an7j0y/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmplht63gm0/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmplht63gm0/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpe3e31xc6/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpe3e31xc6/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp1wgtg1ei/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp1wgtg1ei/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpdh95x0tk/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpdh95x0tk/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpg9yees26/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpg9yees26/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpt1z7du5h/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpt1z7du5h/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp79vafmaf/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp79vafmaf/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmph8e627uz/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmph8e627uz/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpqls3rh3c/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpqls3rh3c/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmphy6f3mzv/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmphy6f3mzv/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpgmij8j5c/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpgmij8j5c/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpj57b6haq/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpj57b6haq/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpecbjzl2l/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpecbjzl2l/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpc2aouek4/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpc2aouek4/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpwbcim91w/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpwbcim91w/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpn60xaprk/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpn60xaprk/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpodr6juzz/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpodr6juzz/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpnku8f7j4/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpnku8f7j4/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp3k0c3xgx/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp3k0c3xgx/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpzzmszzmf/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpzzmszzmf/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpmjgwdlxg/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpmjgwdlxg/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpp8qx7wab/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpp8qx7wab/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp3me5clei/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp3me5clei/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpvysi72y9/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpvysi72y9/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp0gthfp3t/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp0gthfp3t/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpqvjup9pe/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpqvjup9pe/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp2nczm1ct/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp2nczm1ct/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp6c7k17v8/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp6c7k17v8/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpnbv1i5ll/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpnbv1i5ll/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp3mem0vrv/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp3mem0vrv/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpd5_eqdee/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpd5_eqdee/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmprrhcjj1s/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmprrhcjj1s/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmplrsp7nsn/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmplrsp7nsn/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpfi8_dqnz/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpfi8_dqnz/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpcjba205q/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpcjba205q/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp3x4xl8kx/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp3x4xl8kx/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmptl4mij50/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmptl4mij50/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpnri882eq/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpnri882eq/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpf4mjtdvb/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpf4mjtdvb/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp5bxydcr_/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp5bxydcr_/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpsngek_o9/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpsngek_o9/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp5rwxnlsm/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp5rwxnlsm/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp3reaxuh7/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp3reaxuh7/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp5f7newt5/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp5f7newt5/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp24gpxgew/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp24gpxgew/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmppu_ujanc/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmppu_ujanc/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpphosx1mj/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpphosx1mj/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp2ewsipq5/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp2ewsipq5/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpdoi02k_f/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpdoi02k_f/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpwm0rzwa9/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpwm0rzwa9/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp31wk25r8/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp31wk25r8/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpinvwdy28/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpinvwdy28/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpzyeja7zo/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpzyeja7zo/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpd95d2vho/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpd95d2vho/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp5xu7o57h/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp5xu7o57h/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmprxm1chpu/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmprxm1chpu/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp736_445o/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp736_445o/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpo0wqsgl6/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpo0wqsgl6/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpw6jqq74n/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpw6jqq74n/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpzhzzejzw/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpzhzzejzw/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmprmduojf9/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmprmduojf9/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpvsggra0y/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpvsggra0y/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpz9f12yba/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpz9f12yba/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpgmbd99lf/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpgmbd99lf/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp4ruzz0_l/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp4ruzz0_l/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmplkd2mry0/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmplkd2mry0/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp2d9g5x8q/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp2d9g5x8q/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpnl_5tm6n/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpnl_5tm6n/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpa98vpamk/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpa98vpamk/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpdlxtl4ts/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpdlxtl4ts/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmppach67v0/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmppach67v0/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpbo5unal4/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpbo5unal4/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmprafz1wl_/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmprafz1wl_/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpu3j0f9q0/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpu3j0f9q0/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp8gpnqqnl/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp8gpnqqnl/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmptowajn54/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmptowajn54/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpw9p1ahzo/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpw9p1ahzo/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp_c_f42hs/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp_c_f42hs/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpdz9gx_w8/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpdz9gx_w8/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp5hq0h6vz/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp5hq0h6vz/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpj0jjlrwk/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpj0jjlrwk/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpm2fnmbbu/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpm2fnmbbu/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp1vjh62ae/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp1vjh62ae/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpqmj96drf/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpqmj96drf/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpjrkxpdit/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpjrkxpdit/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpw0opbgta/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpw0opbgta/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpe16tesdk/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpe16tesdk/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpbcmieus8/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpbcmieus8/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp77t4tvvo/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp77t4tvvo/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpymmxvarh/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpymmxvarh/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp3zp6xirn/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp3zp6xirn/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp77bkgdj6/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp77bkgdj6/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpon7m77qc/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpon7m77qc/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmphnoidf8v/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmphnoidf8v/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpl5vgy0jt/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpl5vgy0jt/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpm5v33x_x/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpm5v33x_x/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp1ng7lt1n/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp1ng7lt1n/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpct_ujh95/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpct_ujh95/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpf3x5aat5/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpf3x5aat5/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp4ve8_xw2/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp4ve8_xw2/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpm3qt9hgd/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpm3qt9hgd/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpm8puii31/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpm8puii31/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpjju6jkia/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpjju6jkia/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpjgpd82yj/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpjgpd82yj/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpq2yhvk8f/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpq2yhvk8f/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp15qrwqaz/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp15qrwqaz/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmptducohv_/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmptducohv_/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpgt0xivw2/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpgt0xivw2/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpzxyxqaqr/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpzxyxqaqr/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp5md7gycr/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp5md7gycr/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpeczosmol/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpeczosmol/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmph1m_q4jl/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmph1m_q4jl/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp2acsw6zw/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp2acsw6zw/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp8vhtik3o/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp8vhtik3o/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmps2vik80a/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmps2vik80a/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpvhrni1ad/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpvhrni1ad/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpz5d1ar_p/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpz5d1ar_p/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmphs44f80h/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmphs44f80h/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpstndnber/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpstndnber/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp_zbighr3/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp_zbighr3/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp0l_8sspt/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp0l_8sspt/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpwsrxldbq/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpwsrxldbq/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpvt5xk5t6/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpvt5xk5t6/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmps29km0qj/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmps29km0qj/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpbmejwowv/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpbmejwowv/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpb_qucopr/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpb_qucopr/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp6y_q0y_w/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp6y_q0y_w/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpzj8xfbat/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpzj8xfbat/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpsvpbayvw/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpsvpbayvw/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp93a_bji9/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp93a_bji9/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpvp_0nh1r/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpvp_0nh1r/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpoe7v4mnj/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpoe7v4mnj/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp6nx0b7cn/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp6nx0b7cn/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp39g7ldnd/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp39g7ldnd/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp1yc2ji_6/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp1yc2ji_6/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpf3ku2_rc/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpf3ku2_rc/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpuefsbsvw/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpuefsbsvw/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpei8ts8a8/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpei8ts8a8/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpasgx9fou/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpasgx9fou/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpwi2d6lgd/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpwi2d6lgd/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmprb6shyjw/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmprb6shyjw/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpaxvfibo5/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpaxvfibo5/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp1p_xoxg3/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp1p_xoxg3/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpwa230upt/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpwa230upt/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpiknkfpgl/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpiknkfpgl/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp2s4xr1zp/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp2s4xr1zp/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpii6uuk5b/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpii6uuk5b/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpgkmkmo63/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpgkmkmo63/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp4e89c7jx/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp4e89c7jx/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp5ax196a_/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp5ax196a_/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpbyxi0wo8/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpbyxi0wo8/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpeon7i_2o/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpeon7i_2o/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpvz0f_ab_/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpvz0f_ab_/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpzvypkq0h/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpzvypkq0h/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpjqorl__a/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpjqorl__a/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpg3jxxafv/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpg3jxxafv/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpkhu4rav0/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpkhu4rav0/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp_wuf0kth/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp_wuf0kth/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpxo9u4f86/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpxo9u4f86/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp5a7uaiba/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp5a7uaiba/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpu3wgfqzp/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpu3wgfqzp/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpp3494xi4/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpp3494xi4/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpeb77x7pz/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpeb77x7pz/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpats6gdy4/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpats6gdy4/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpvukv44jz/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpvukv44jz/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpat_hhz19/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpat_hhz19/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp1x9ww4_g/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp1x9ww4_g/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpugwnujfo/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpugwnujfo/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp4bmyfx50/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp4bmyfx50/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpakxcb8md/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpakxcb8md/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpebvpwe0z/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpebvpwe0z/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpntukg91x/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpntukg91x/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp_nxthbwi/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp_nxthbwi/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpwru8y8ss/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpwru8y8ss/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpz5vhvbqw/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpz5vhvbqw/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpa1rbhky3/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpa1rbhky3/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpw6dk5vol/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpw6dk5vol/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpoewbcw06/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpoewbcw06/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpy7hde3ca/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpy7hde3ca/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpraz6s7p0/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpraz6s7p0/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmplcl9uv0g/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmplcl9uv0g/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpbicd0nlp/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpbicd0nlp/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpswk7d59j/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpswk7d59j/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpe_xfzzeg/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpe_xfzzeg/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpzhli9q_g/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpzhli9q_g/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpgq5hp_ev/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpgq5hp_ev/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp7akj2wwc/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp7akj2wwc/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpxmf1zpxm/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpxmf1zpxm/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpaqnzlmf_/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpaqnzlmf_/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmphjsvnumc/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmphjsvnumc/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp5ue10wwg/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp5ue10wwg/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpk0op12ii/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpk0op12ii/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpo96pl28j/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpo96pl28j/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp1uyghcj3/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp1uyghcj3/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpo7c_3m3m/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpo7c_3m3m/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmppp464d20/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmppp464d20/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpdn5isg54/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpdn5isg54/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpmy4nib1k/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpmy4nib1k/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpemnqt0uf/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpemnqt0uf/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpsa6vjgzv/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpsa6vjgzv/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpw28nfjvc/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpw28nfjvc/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpgzsl3nek/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpgzsl3nek/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpigoevove/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpigoevove/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpx_bu7oy6/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpx_bu7oy6/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpxfs2dz8q/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpxfs2dz8q/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpql_17780/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpql_17780/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp02x85p94/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp02x85p94/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpl048yj1b/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpl048yj1b/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp06y8hdqr/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp06y8hdqr/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpzz9wyy_s/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpzz9wyy_s/f2.bed | bedtools merge -c 4,5,6 -o first -i -) ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. _____________________________ test_coverage[same] ______________________________ [gw1] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness = 'same' @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness", strandedness) tests/test_binary.py:207: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:238: in test_coverage result = gr.coverage(gr2, strandedness=strandedness) pyranges/pyranges.py:1341: in coverage other = other.merge(count=True, strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_coverage( E strandedness='same', E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., # or any other generated value E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., # or any other generated value E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2TABIxYxAAAZAAD') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmppyxeg5xs/f1.bed -b /tmp/tmppyxeg5xs/f2.bed Chromosome Start End Name Score Strand 0 chr1 8132692 8137479 a 0 + 1 chr1 2 4162 a 0 + 2 chr1 6631560 6639879 a 0 + 3 chr1 4363346 4371296 a 0 - 4 chr1 1752342 1762245 a 0 - 5 chr6 3566774 3575003 a 0 - 6 chr8 1055568 1057990 a 0 - 7 chr11 8373096 8382652 a 0 - 8 chr19 3569883 3570575 a 0 + Chromosome Start End Name Score Strand 0 chr21 9078828 9088751 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpklwdjhvw/f1.bed -b /tmp/tmpklwdjhvw/f2.bed Chromosome Start End Name Score Strand 0 chr21 9078828 9088751 a 0 + Chromosome Start End Name Score Strand 0 chr21 9078828 9088751 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpk9zm4zpu/f1.bed -b /tmp/tmpk9zm4zpu/f2.bed Chromosome Start End Name Score Strand 0 chr21 9923 19846 a 0 + Chromosome Start End Name Score Strand 0 chr21 9078828 9088751 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpm065lw60/f1.bed -b /tmp/tmpm065lw60/f2.bed Chromosome Start End Name Score Strand 0 chr21 9923 19846 a 0 + Chromosome Start End Name Score Strand 0 chr21 9078828 9088751 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp5mjcyps5/f1.bed -b /tmp/tmp5mjcyps5/f2.bed Chromosome Start End Name Score Strand 0 chr21 9923 19846 a 0 + Chromosome Start End Name Score Strand 0 chr1 9078828 9088751 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmphopl3m6b/f1.bed -b /tmp/tmphopl3m6b/f2.bed Chromosome Start End Name Score Strand 0 chr21 9923 19846 a 0 + Chromosome Start End Name Score Strand 0 chr1 9078828 9088751 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpc9negj0_/f1.bed -b /tmp/tmpc9negj0_/f2.bed Chromosome Start End Name Score Strand 0 chr1 2946635 2949923 a 0 + 1 chr1 7312900 7320252 a 0 - Chromosome Start End Name Score Strand 0 chr1 8719232 8727617 a 0 + 1 chr1 6653825 6657826 a 0 + 2 chr1 9761963 9765114 a 0 + 3 chr1 9761963 9768435 a 0 + 4 chr1 9556840 9559622 a 0 + 5 chr1 4726611 4733492 a 0 + 6 chr1 4167623 4173853 a 0 - 7 chr1 9761963 9770112 a 0 - 8 chr1 3781095 3789625 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpv8o0bz8b/f1.bed -b /tmp/tmpv8o0bz8b/f2.bed Chromosome Start End Name Score Strand 0 chr1 2946635 2949923 a 0 + 1 chr1 7312900 7320252 a 0 - Chromosome Start End Name Score Strand 0 chr1 8719232 8727617 a 0 + 1 chr1 6653825 6657826 a 0 + 2 chr1 9761963 9765114 a 0 + 3 chr1 9761963 9768435 a 0 + 4 chr1 9556840 9559622 a 0 + 5 chr1 4726611 4733492 a 0 + 6 chr1 4167623 4173853 a 0 - 7 chr1 9761963 9770112 a 0 - 8 chr1 3781095 3783175 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpqpv7m1ia/f1.bed -b /tmp/tmpqpv7m1ia/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpw3i0pk37/f1.bed -b /tmp/tmpw3i0pk37/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp0jzmsv1q/f1.bed -b /tmp/tmp0jzmsv1q/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmplso_6qnr/f1.bed -b /tmp/tmplso_6qnr/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp0nnuvnta/f1.bed -b /tmp/tmp0nnuvnta/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpsz9s89oc/f1.bed -b /tmp/tmpsz9s89oc/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpy_mggjs7/f1.bed -b /tmp/tmpy_mggjs7/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp6rxy4spm/f1.bed -b /tmp/tmp6rxy4spm/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpghz0v6k5/f1.bed -b /tmp/tmpghz0v6k5/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + 4 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 709796 711628 a 0 + 1 chr1 8867161 8875801 a 0 - 2 chr1 9556789 9563265 a 0 - 3 chr12 150341 152572 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpr0z1eq1r/f1.bed -b /tmp/tmpr0z1eq1r/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + 4 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpv8ufrntf/f1.bed -b /tmp/tmpv8ufrntf/f2.bed Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 + 1 chr20 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1929539 1937020 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp0m5pf_04/f1.bed -b /tmp/tmp0m5pf_04/f2.bed Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 + 1 chr20 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpnl8po5nu/f1.bed -b /tmp/tmpnl8po5nu/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 5563108 5565295 a 0 + 1 chr1 5563108 5570022 a 0 + 2 chr1 1247590 1250425 a 0 - 3 chr1 5563108 5572945 a 0 - 4 chr5 5563108 5565943 a 0 - 5 chr8 5563108 5565943 a 0 - 6 chr11 8010472 8011163 a 0 - 7 chr13 5563108 5565943 a 0 + 8 chr18 5563108 5565943 a 0 - 9 chr18 3078928 3081763 a 0 - 10 chr21 6781459 6784294 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp65arch83/f1.bed -b /tmp/tmp65arch83/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpbxh2o8nw/f1.bed -b /tmp/tmpbxh2o8nw/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1734680 1739613 a 0 + 1 chr1 3774142 3778661 a 0 - 2 chr6 4508113 4510154 a 0 + 3 chr13 7813582 7816428 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpkulfvgq2/f1.bed -b /tmp/tmpkulfvgq2/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpueuj3adb/f1.bed -b /tmp/tmpueuj3adb/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 143827 148323 a 0 - 1 chr17 3576276 3580772 a 0 - 2 chrX 3650018 3654514 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpdemu2hfa/f1.bed -b /tmp/tmpdemu2hfa/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpew7p6ksx/f1.bed -b /tmp/tmpew7p6ksx/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr3 9999999 10008494 a 0 + 1 chr14 3939608 3945352 a 0 + 2 chr14 9999999 10000818 a 0 + 3 chr14 9999999 10007801 a 0 - 4 chr20 7221924 7230419 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp7knce_p1/f1.bed -b /tmp/tmp7knce_p1/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpb6d5l7qc/f1.bed -b /tmp/tmpb6d5l7qc/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 3854402 3858370 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp2ht8w2_1/f1.bed -b /tmp/tmp2ht8w2_1/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpmdhstcfk/f1.bed -b /tmp/tmpmdhstcfk/f2.bed Chromosome Start End Name Score Strand 0 chr1 2121401 2121658 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 1309 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp3zd78opb/f1.bed -b /tmp/tmp3zd78opb/f2.bed Chromosome Start End Name Score Strand 0 chr1 2121401 2121658 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpekvowwls/f1.bed -b /tmp/tmpekvowwls/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 645915 649378 a 0 + 1 chr1 1763835 1770794 a 0 - 2 chr1 5705768 5715006 a 0 - 3 chr11 9999999 10009998 a 0 - 4 chr13 9091579 9091580 a 0 + 5 chr14 1763835 1769907 a 0 - 6 chr15 2347684 2351625 a 0 + 7 chr16 5082443 5087811 a 0 + 8 chr20 1763835 1773402 a 0 + 9 chr22 1458394 1466726 a 0 - 10 chrY 1763835 1768098 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpq8oe2kcz/f1.bed -b /tmp/tmpq8oe2kcz/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp9f6ogtcu/f1.bed -b /tmp/tmp9f6ogtcu/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + 4 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 9248 a 0 - 1 chr15 6976445 6984416 a 0 + 2 chr21 1247366 1256096 a 0 + 3 chrM 1435945 1445945 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpotopxpjb/f1.bed -b /tmp/tmpotopxpjb/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + 4 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpf860bn4s/f1.bed -b /tmp/tmpf860bn4s/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 5472159 5479479 a 0 + 1 chr1 5472159 5479479 a 0 + 2 chr1 5472159 5479479 a 0 + 3 chr1 5472159 5479479 a 0 + 4 chr1 5472159 5477036 a 0 - 5 chr1 5472159 5479479 a 0 - 6 chr2 5472159 5479479 a 0 - 7 chr3 5472159 5473108 a 0 + 8 chr7 5472159 5479479 a 0 + 9 chr20 5472159 5479479 a 0 + 10 chrM 5472159 5479479 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpo0b__3ea/f1.bed -b /tmp/tmpo0b__3ea/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpfgsyiwun/f1.bed -b /tmp/tmpfgsyiwun/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 3583240 3589550 a 0 - 1 chr1 7139337 7140343 a 0 - 2 chr22 26689 32118 a 0 + 3 chr22 10000000 10009841 a 0 + 4 chr22 8087428 8088455 a 0 + 5 chr22 2120912 2128953 a 0 - 6 chr22 3296958 3297128 a 0 - 7 chr22 4785901 4787691 a 0 - 8 chr22 612883 620806 a 0 - 9 chrX 1427845 1437409 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp0l95fgov/f1.bed -b /tmp/tmp0l95fgov/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpige8j3i_/f1.bed -b /tmp/tmpige8j3i_/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 8212217 8221751 a 0 + 1 chr1 9486361 9494314 a 0 - 2 chr1 1813426 1822960 a 0 - 3 chr1 6837610 6838902 a 0 - 4 chr1 2381223 2383945 a 0 - 5 chr18 74753 84287 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpvp4dz5hl/f1.bed -b /tmp/tmpvp4dz5hl/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp3r8h2_kt/f1.bed -b /tmp/tmp3r8h2_kt/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 5725020 5733870 a 0 - 1 chr4 6754690 6758504 a 0 - 2 chr12 7626239 7635044 a 0 + 3 chrY 8358221 8362139 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp1m69x693/f1.bed -b /tmp/tmp1m69x693/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp3gdy85tv/f1.bed -b /tmp/tmp3gdy85tv/f2.bed Chromosome Start End Name Score Strand 0 chrX 8978951 8978952 a 0 + Chromosome Start End Name Score Strand 0 chr1 9240 16627 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpq4iypr1v/f1.bed -b /tmp/tmpq4iypr1v/f2.bed Chromosome Start End Name Score Strand 0 chrX 8978951 8978952 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpi6p__2zy/f1.bed -b /tmp/tmpi6p__2zy/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr17 3342358 3347637 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp2en6ija9/f1.bed -b /tmp/tmp2en6ija9/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpmnrxowfo/f1.bed -b /tmp/tmpmnrxowfo/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 8857908 8865132 a 0 + 1 chr1 9049190 9051990 a 0 + 2 chr1 9110454 9111623 a 0 - 3 chr10 8181767 8190619 a 0 - 4 chr18 3232329 3237872 a 0 + 5 chr21 6262539 6266323 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp9eue9omr/f1.bed -b /tmp/tmp9eue9omr/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpl0db5hda/f1.bed -b /tmp/tmpl0db5hda/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 2135144 2135707 a 0 + 1 chr1 9447562 9457435 a 0 + 2 chr1 2381589 2384050 a 0 + 3 chr1 4640225 4641822 a 0 + 4 chr1 3113633 3117878 a 0 + 5 chr1 2582256 2584642 a 0 + 6 chr1 9956413 9960174 a 0 - 7 chr1 2343758 2351748 a 0 - 8 chr11 9999999 10002641 a 0 - 9 chr12 4473531 4477635 a 0 + 10 chrY 5597765 5603290 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp_5o88hzj/f1.bed -b /tmp/tmp_5o88hzj/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpkrbykst_/f1.bed -b /tmp/tmpkrbykst_/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 2546441 2555849 a 0 + 1 chr1 6488500 6495028 a 0 + 2 chr1 4323010 4325684 a 0 + 3 chr1 9799134 9809018 a 0 + 4 chr1 1783364 1787052 a 0 + 5 chr1 2523968 2528836 a 0 - 6 chr1 4441306 4447308 a 0 - 7 chr1 6401562 6410064 a 0 - 8 chr14 6638721 6647522 a 0 - 9 chr21 2546441 2550285 a 0 - 10 chrM 566454 575770 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpaz0w_fks/f1.bed -b /tmp/tmpaz0w_fks/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpqolu4ocd/f1.bed -b /tmp/tmpqolu4ocd/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 3727451 3735232 a 0 + 1 chr1 3406913 3410881 a 0 + 2 chr1 9532772 9533801 a 0 - 3 chr1 10000000 10000222 a 0 - 4 chr1 6202421 6203449 a 0 - 5 chr1 5019491 5027848 a 0 - 6 chr1 3399512 3409322 a 0 - 7 chr4 2893304 2895381 a 0 - 8 chr8 9161869 9164311 a 0 - 9 chr11 2474650 2475191 a 0 + 10 chr21 3390118 3390120 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpidoo7wnj/f1.bed -b /tmp/tmpidoo7wnj/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpb6_7we6i/f1.bed -b /tmp/tmpb6_7we6i/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1646508 1651087 a 0 + 1 chr1 1332537 1337321 a 0 + 2 chr1 3295466 3303818 a 0 - 3 chr1 3424122 3428116 a 0 - 4 chr4 1511823 1514588 a 0 + 5 chr9 818420 826242 a 0 - 6 chr12 2777435 2784024 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpc0d0_nbf/f1.bed -b /tmp/tmpc0d0_nbf/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp8tkol0n7/f1.bed -b /tmp/tmp8tkol0n7/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 874969 883343 a 0 - 1 chr2 8334873 8342632 a 0 - 2 chr14 6993674 7000646 a 0 - 3 chrY 5903764 5908315 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmptc4d6gw8/f1.bed -b /tmp/tmptc4d6gw8/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpk83xwlsw/f1.bed -b /tmp/tmpk83xwlsw/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 9529016 9529585 a 0 + 1 chr20 2871822 2872732 a 0 - 2 chrY 6973926 6983118 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpcznunc1z/f1.bed -b /tmp/tmpcznunc1z/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp4tu9vxky/f1.bed -b /tmp/tmp4tu9vxky/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 6847106 6853783 a 0 + 1 chr1 9410420 9420231 a 0 + 2 chr1 8642907 8646323 a 0 - 3 chr1 3009717 3018844 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp1iev9al5/f1.bed -b /tmp/tmp1iev9al5/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpldoxm1w4/f1.bed -b /tmp/tmpldoxm1w4/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chrM 6916502 6924925 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp_os6pvcc/f1.bed -b /tmp/tmp_os6pvcc/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpw4232851/f1.bed -b /tmp/tmpw4232851/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 3582619 3582621 a 0 + 1 chr1 8139605 8139607 a 0 - 2 chr1 9999999 10000001 a 0 - 3 chr1 4743826 4743828 a 0 - 4 chr1 9443784 9443786 a 0 - 5 chr1 8633823 8633825 a 0 - 6 chr3 1372191 1372193 a 0 + 7 chr9 7845982 7845984 a 0 - 8 chr13 6134606 6134608 a 0 - 9 chr20 1131706 1131708 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpzb5cb19n/f1.bed -b /tmp/tmpzb5cb19n/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpkmr05qr6/f1.bed -b /tmp/tmpkmr05qr6/f2.bed Chromosome Start End Name Score Strand 0 chrX 4988842 4988843 a 0 + Chromosome Start End Name Score Strand 0 chr1 112 7535 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpnpf6raqh/f1.bed -b /tmp/tmpnpf6raqh/f2.bed Chromosome Start End Name Score Strand 0 chrX 4988842 4988843 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpu1vb5sid/f1.bed -b /tmp/tmpu1vb5sid/f2.bed Chromosome Start End Name Score Strand 0 chr3 3014913 3014914 a 0 + Chromosome Start End Name Score Strand 0 chr1 1317007 1317969 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpj_w82fxv/f1.bed -b /tmp/tmpj_w82fxv/f2.bed Chromosome Start End Name Score Strand 0 chr3 3014913 3014914 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpr43mq3gw/f1.bed -b /tmp/tmpr43mq3gw/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 3046304 3054104 a 0 - 1 chr1 6937902 6940230 a 0 - 2 chr6 1448473 1450535 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpvfmjpbvi/f1.bed -b /tmp/tmpvfmjpbvi/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpe2rfpr1r/f1.bed -b /tmp/tmpe2rfpr1r/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 9771462 9776167 a 0 - 1 chr16 5444936 5449148 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpd6hxsf5r/f1.bed -b /tmp/tmpd6hxsf5r/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpdv09km5s/f1.bed -b /tmp/tmpdv09km5s/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 590269 599376 a 0 + 1 chr22 1250869 1255949 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpkunqa6t7/f1.bed -b /tmp/tmpkunqa6t7/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpp_n7w_kb/f1.bed -b /tmp/tmpp_n7w_kb/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 4532203 4541146 a 0 + 1 chr1 4046022 4052043 a 0 - 2 chr1 5562429 5571372 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp0ajedcdr/f1.bed -b /tmp/tmp0ajedcdr/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpifu1034v/f1.bed -b /tmp/tmpifu1034v/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 8794504 8795302 a 0 + 1 chr21 103697 109467 a 0 + 2 chr21 2208079 2211472 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpqcwnkd8v/f1.bed -b /tmp/tmpqcwnkd8v/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpjqztvi_g/f1.bed -b /tmp/tmpjqztvi_g/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + 4 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 3303963 3313963 a 0 + 1 chr1 6698076 6702026 a 0 - 2 chr6 8719951 8725597 a 0 + 3 chr6 9685764 9693209 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpeycb6sij/f1.bed -b /tmp/tmpeycb6sij/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + 4 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmppo5fi6ve/f1.bed -b /tmp/tmppo5fi6ve/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 6230224 6233518 a 0 + 1 chr1 1847501 1856515 a 0 - 2 chr1 9619310 9624417 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp0jiooloy/f1.bed -b /tmp/tmp0jiooloy/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp1y6bymhc/f1.bed -b /tmp/tmp1y6bymhc/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr12 9942232 9948665 a 0 + 1 chr15 4635045 4642844 a 0 + 2 chr15 6154356 6157742 a 0 + 3 chr15 3969640 3975030 a 0 - 4 chrM 1130576 1140153 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpne9axlg4/f1.bed -b /tmp/tmpne9axlg4/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp42zv7x88/f1.bed -b /tmp/tmp42zv7x88/f2.bed Chromosome Start End Name Score Strand 0 chr3 65537 65538 a 0 + Chromosome Start End Name Score Strand 0 chr1 3453253 3458176 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpu9dr4b3p/f1.bed -b /tmp/tmpu9dr4b3p/f2.bed Chromosome Start End Name Score Strand 0 chr3 65537 65538 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpw59lowsn/f1.bed -b /tmp/tmpw59lowsn/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 4307753 4314108 a 0 - 1 chr11 7723972 7731526 a 0 - 2 chr18 4307753 4313456 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpbrkqv0cp/f1.bed -b /tmp/tmpbrkqv0cp/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp5bbrajwz/f1.bed -b /tmp/tmp5bbrajwz/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1343807 1348276 a 0 + 1 chr12 1962607 1964749 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpu5mir4bm/f1.bed -b /tmp/tmpu5mir4bm/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp93p4xjw6/f1.bed -b /tmp/tmp93p4xjw6/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1243726 1251177 a 0 + 1 chr1 6481571 6484212 a 0 + 2 chr1 1721279 1722038 a 0 + 3 chr1 6437411 6440663 a 0 - 4 chr1 8333268 8333269 a 0 - 5 chr10 3848226 3856368 a 0 - 6 chr12 8333268 8343267 a 0 + 7 chr12 8333268 8340171 a 0 + 8 chr12 8333268 8338669 a 0 + 9 chr12 8333268 8339932 a 0 - 10 chr17 8333268 8340413 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpxi619t1j/f1.bed -b /tmp/tmpxi619t1j/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp0mylckxt/f1.bed -b /tmp/tmp0mylckxt/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 8314301 8319930 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmphip3d5ou/f1.bed -b /tmp/tmphip3d5ou/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmptdfmfaex/f1.bed -b /tmp/tmptdfmfaex/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 4617257 4617352 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmprrnsle04/f1.bed -b /tmp/tmprrnsle04/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp2cywmmdr/f1.bed -b /tmp/tmp2cywmmdr/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr16 6190824 6192279 a 0 + 1 chr16 1900907 1908762 a 0 + 2 chr16 3355155 3360666 a 0 + 3 chr16 7407592 7413892 a 0 + 4 chr16 5193735 5194847 a 0 - 5 chr16 4674164 4683576 a 0 - 6 chr16 4449600 4458985 a 0 - 7 chr16 5476695 5485207 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp0pwu8qlw/f1.bed -b /tmp/tmp0pwu8qlw/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpo39zua1n/f1.bed -b /tmp/tmpo39zua1n/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 5955817 5964823 a 0 + 1 chr1 5955817 5961336 a 0 + 2 chr1 5955817 5963904 a 0 + 3 chr1 5955817 5962334 a 0 - 4 chr1 4742621 4743301 a 0 - 5 chr1 5955817 5962973 a 0 - 6 chr2 5955817 5964847 a 0 - 7 chr14 5955817 5957354 a 0 + 8 chr20 5955817 5958021 a 0 + 9 chr21 5955817 5957975 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpix4sukt1/f1.bed -b /tmp/tmpix4sukt1/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpio_t38h_/f1.bed -b /tmp/tmpio_t38h_/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 2065276 2072565 a 0 - 1 chr11 318178 325641 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp7ziic4y9/f1.bed -b /tmp/tmp7ziic4y9/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmph2pq1lf0/f1.bed -b /tmp/tmph2pq1lf0/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr9 7103697 7104913 a 0 + 1 chr16 2899408 2906341 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpm2d4hnpm/f1.bed -b /tmp/tmpm2d4hnpm/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpcca5wfnq/f1.bed -b /tmp/tmpcca5wfnq/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr2 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 5829642 5833587 a 0 + 1 chr1 1935363 1939837 a 0 - 2 chr11 5829642 5838214 a 0 + 3 chr15 5829642 5830938 a 0 + 4 chr22 8927408 8930919 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpkxwqmags/f1.bed -b /tmp/tmpkxwqmags/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr2 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpdsvoti3n/f1.bed -b /tmp/tmpdsvoti3n/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 2478968 2488650 a 0 - 1 chr13 3819810 3822745 a 0 - 2 chr14 2478968 2478970 a 0 - 3 chr19 2705156 2708597 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpl7xjh8u4/f1.bed -b /tmp/tmpl7xjh8u4/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp2ksdv3is/f1.bed -b /tmp/tmp2ksdv3is/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 301311 305219 a 0 + 1 chr1 5259689 5261689 a 0 + 2 chr1 3367363 3368564 a 0 + 3 chr1 4992400 4999161 a 0 - 4 chr2 2393371 2397045 a 0 + 5 chr5 5711008 5713029 a 0 + 6 chr5 1451633 1451880 a 0 - 7 chr7 800573 805675 a 0 + 8 chr15 9355065 9364902 a 0 - 9 chr18 689132 689135 a 0 + 10 chrY 116709 121069 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpp5k829_z/f1.bed -b /tmp/tmpp5k829_z/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp11wgj4ms/f1.bed -b /tmp/tmp11wgj4ms/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 961710 971659 a 0 - 1 chr15 6974486 6976732 a 0 - 2 chr22 673974 678278 a 0 + 3 chr22 8406691 8411478 a 0 + 4 chr22 8982220 8984399 a 0 + 5 chr22 172855 175118 a 0 + 6 chr22 3389139 3397235 a 0 + 7 chr22 9408796 9411825 a 0 + 8 chr22 6792452 6800454 a 0 - 9 chr22 961710 968898 a 0 - 10 chr22 9991123 9999930 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmppd0mrh52/f1.bed -b /tmp/tmppd0mrh52/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpi21g1ocs/f1.bed -b /tmp/tmpi21g1ocs/f2.bed Chromosome Start End Name Score Strand 0 chr7 5869885 5869886 a 0 + Chromosome Start End Name Score Strand 0 chr1 16 3882 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpj1223fmj/f1.bed -b /tmp/tmpj1223fmj/f2.bed Chromosome Start End Name Score Strand 0 chr7 5869885 5869886 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpxi5e60g0/f1.bed -b /tmp/tmpxi5e60g0/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 6029569 6029570 a 0 + Chromosome Start End Name Score Strand 0 chr1 8154937 8157244 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpdxccwqjc/f1.bed -b /tmp/tmpdxccwqjc/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 6029569 6029570 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp7ymgkfnm/f1.bed -b /tmp/tmp7ymgkfnm/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr12 5512137 5513528 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpzyll0u_5/f1.bed -b /tmp/tmpzyll0u_5/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp9xzdmb1m/f1.bed -b /tmp/tmp9xzdmb1m/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 6723968 6733405 a 0 + 1 chr1 5318620 5326159 a 0 + 2 chr1 5834864 5840760 a 0 - 3 chr1 3401682 3401683 a 0 - 4 chr9 7397263 7402052 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp55yj3wul/f1.bed -b /tmp/tmp55yj3wul/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp296mfrt1/f1.bed -b /tmp/tmp296mfrt1/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 4240609 4241050 a 0 + 1 chr1 922716 928709 a 0 + 2 chr1 9323072 9332483 a 0 - 3 chr1 8342812 8352765 a 0 - 4 chr1 2465347 2471252 a 0 - 5 chr5 8533230 8539516 a 0 - 6 chr15 7515363 7520086 a 0 + 7 chr15 663003 669301 a 0 + 8 chr20 1435198 1440943 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp85y98gf9/f1.bed -b /tmp/tmp85y98gf9/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpk0dih6nu/f1.bed -b /tmp/tmpk0dih6nu/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr18 9290380 9290381 a 0 - 1 chr18 2248150 2257581 a 0 - 2 chr18 2354157 2359228 a 0 - 3 chr18 8515539 8523310 a 0 - 4 chr18 826326 829651 a 0 - 5 chr18 694401 700684 a 0 - 6 chr18 3711307 3716129 a 0 - 7 chr18 1770223 1774021 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpjyzvcocf/f1.bed -b /tmp/tmpjyzvcocf/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp567363mt/f1.bed -b /tmp/tmp567363mt/f2.bed Chromosome Start End Name Score Strand 0 chr1 8198369 8198370 a 0 + Chromosome Start End Name Score Strand 0 chr1 60589 69390 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpctwx9tkw/f1.bed -b /tmp/tmpctwx9tkw/f2.bed Chromosome Start End Name Score Strand 0 chr1 8198369 8198370 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpohkwpf6i/f1.bed -b /tmp/tmpohkwpf6i/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 8805255 8811647 a 0 + 1 chr1 7433001 7439724 a 0 - 2 chr1 244542 246304 a 0 - 3 chr1 8088198 8094590 a 0 - 4 chr1 1003296 1011627 a 0 - 5 chr1 252702 259592 a 0 - 6 chr1 5028085 5033330 a 0 - 7 chr2 7958976 7964129 a 0 - 8 chr4 9331456 9339092 a 0 - 9 chr15 252702 256188 a 0 - 10 chr15 7127089 7127715 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpsmfwpku4/f1.bed -b /tmp/tmpsmfwpku4/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp4xf0_foz/f1.bed -b /tmp/tmp4xf0_foz/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 5139819 5142751 a 0 + 1 chr1 4584134 4586266 a 0 + 2 chr1 5139819 5140153 a 0 + 3 chr1 5139819 5147196 a 0 + 4 chr1 5139819 5140829 a 0 - 5 chr1 5228322 5234512 a 0 - 6 chr1 5139819 5148123 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpwfqcedtn/f1.bed -b /tmp/tmpwfqcedtn/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpq8od6p7u/f1.bed -b /tmp/tmpq8od6p7u/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr19 1 2 a 0 + Chromosome Start End Name Score Strand 0 chrX 9541562 9542328 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpkjyvt98x/f1.bed -b /tmp/tmpkjyvt98x/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr19 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpc1d99yxa/f1.bed -b /tmp/tmpc1d99yxa/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 4463479 4467296 a 0 - 1 chr1 253205 255751 a 0 - 2 chr18 9510754 9513569 a 0 + 3 chr18 1813913 1816459 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpt7gv6a0l/f1.bed -b /tmp/tmpt7gv6a0l/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpcyqskn30/f1.bed -b /tmp/tmpcyqskn30/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 3692303 3694965 a 0 + 1 chr1 1916034 1917370 a 0 + 2 chr1 9999999 10000764 a 0 + 3 chr1 3473886 3476392 a 0 - 4 chr1 2776384 2780105 a 0 - 5 chr1 7933082 7934859 a 0 - 6 chr1 5938218 5945597 a 0 - 7 chr1 8172370 8179450 a 0 - 8 chr8 1636089 1646089 a 0 - 9 chr14 1916720 1920807 a 0 + 10 chr17 3692303 3694784 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpkga_jifh/f1.bed -b /tmp/tmpkga_jifh/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp4v5hpkpa/f1.bed -b /tmp/tmp4v5hpkpa/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 3526940 3528943 a 0 + 1 chr1 3720618 3729505 a 0 + 2 chr1 9730705 9739698 a 0 + 3 chr1 3637308 3642976 a 0 + 4 chr1 8501313 8509691 a 0 + 5 chr1 2446016 2454463 a 0 + 6 chr1 9839053 9840501 a 0 + 7 chr1 3859702 3864824 a 0 - 8 chr8 870137 877825 a 0 + 9 chr9 2958192 2968096 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpojuhe4lb/f1.bed -b /tmp/tmpojuhe4lb/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpzkdzgzvc/f1.bed -b /tmp/tmpzkdzgzvc/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 9967913 9971017 a 0 - 1 chr1 2447705 2457335 a 0 - 2 chr1 3937665 3946141 a 0 - 3 chr1 3785668 3788166 a 0 - 4 chr17 8170072 8172727 a 0 + 5 chr20 8523902 8532910 a 0 - 6 chrX 5900010 5905100 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp83_fwg0r/f1.bed -b /tmp/tmp83_fwg0r/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmps79c6yef/f1.bed -b /tmp/tmps79c6yef/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr18 4550394 4555922 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp2uci96d1/f1.bed -b /tmp/tmp2uci96d1/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp2cp4okiu/f1.bed -b /tmp/tmp2cp4okiu/f2.bed Chromosome Start End Name Score Strand 0 chr1 544612 544613 a 0 + Chromosome Start End Name Score Strand 0 chr1 22818 28753 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpgkebfna6/f1.bed -b /tmp/tmpgkebfna6/f2.bed Chromosome Start End Name Score Strand 0 chr1 544612 544613 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpsfqz48zr/f1.bed -b /tmp/tmpsfqz48zr/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 5137354 5139890 a 0 + 1 chr1 3397268 3399804 a 0 + 2 chr1 8977876 8980412 a 0 + 3 chr1 8300340 8302876 a 0 + 4 chr1 9741827 9745119 a 0 - 5 chr1 7406627 7409641 a 0 - 6 chr1 39705 42241 a 0 - 7 chr1 9601011 9603547 a 0 - 8 chr1 1076749 1079285 a 0 - 9 chr18 5258191 5259013 a 0 + 10 chr20 5258191 5260727 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpd78rmze5/f1.bed -b /tmp/tmpd78rmze5/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpxiji76tt/f1.bed -b /tmp/tmpxiji76tt/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 4028384 4035794 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpy592ss6b/f1.bed -b /tmp/tmpy592ss6b/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpkajqfsc1/f1.bed -b /tmp/tmpkajqfsc1/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 6851675 6860882 a 0 + 1 chr1 5086351 5092395 a 0 + 2 chr1 6007509 6015981 a 0 + 3 chr1 5086351 5095970 a 0 + 4 chr1 5086351 5092477 a 0 + 5 chr1 5086351 5094255 a 0 + 6 chr1 5086351 5096040 a 0 - 7 chr1 5086351 5090519 a 0 - 8 chr5 5086351 5087167 a 0 + 9 chr13 2986138 2992996 a 0 + 10 chrY 6901117 6901592 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpzc2e_4g3/f1.bed -b /tmp/tmpzc2e_4g3/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpm7zxxxye/f1.bed -b /tmp/tmpm7zxxxye/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr2 5709942 5713060 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp3qbavz2j/f1.bed -b /tmp/tmp3qbavz2j/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpz9wfunw4/f1.bed -b /tmp/tmpz9wfunw4/f2.bed Chromosome Start End Name Score Strand 0 chr1 56322 56323 a 0 + Chromosome Start End Name Score Strand 0 chr1 14317 16081 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpbqzocgqy/f1.bed -b /tmp/tmpbqzocgqy/f2.bed Chromosome Start End Name Score Strand 0 chr1 56322 56323 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpuoalxstb/f1.bed -b /tmp/tmpuoalxstb/f2.bed Chromosome Start End Name Score Strand 0 chrY 65537 65538 a 0 + Chromosome Start End Name Score Strand 0 chr1 2857001 2867000 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpdo3gjznk/f1.bed -b /tmp/tmpdo3gjznk/f2.bed Chromosome Start End Name Score Strand 0 chrY 65537 65538 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp5i57in9l/f1.bed -b /tmp/tmp5i57in9l/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 9772072 9772073 a 0 - 1 chr13 5148703 5150905 a 0 + 2 chr13 4868385 4868386 a 0 - 3 chr13 3700097 3706000 a 0 - 4 chr13 7642748 7652481 a 0 - 5 chr13 7761813 7761814 a 0 - 6 chr13 3608764 3608765 a 0 - 7 chr13 1340074 1340075 a 0 - 8 chr13 3079675 3084454 a 0 - 9 chr13 650192 650193 a 0 - 10 chrM 53591 57454 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpxn7e4fb2/f1.bed -b /tmp/tmpxn7e4fb2/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp77bz_jpm/f1.bed -b /tmp/tmp77bz_jpm/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 2161622 2169698 a 0 - 1 chr1 4358280 4362754 a 0 - 2 chr1 1647195 1650743 a 0 - 3 chr2 3127656 3137105 a 0 - 4 chr18 2271711 2281304 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpjzd95l37/f1.bed -b /tmp/tmpjzd95l37/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmptrodo6na/f1.bed -b /tmp/tmptrodo6na/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr2 6702596 6708831 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpnkf96qjh/f1.bed -b /tmp/tmpnkf96qjh/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpa_luup21/f1.bed -b /tmp/tmpa_luup21/f2.bed Chromosome Start End Name Score Strand 0 chr11 65537 65538 a 0 + Chromosome Start End Name Score Strand 0 chr1 9562671 9567253 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmphu2m8gw5/f1.bed -b /tmp/tmphu2m8gw5/f2.bed Chromosome Start End Name Score Strand 0 chr11 65537 65538 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpf1vga7c4/f1.bed -b /tmp/tmpf1vga7c4/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2575 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpjdq4sjql/f1.bed -b /tmp/tmpjdq4sjql/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmprzwwzl6q/f1.bed -b /tmp/tmprzwwzl6q/f2.bed Chromosome Start End Name Score Strand 0 chr1 2110753 2111010 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 1655 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpd1jz70nk/f1.bed -b /tmp/tmpd1jz70nk/f2.bed Chromosome Start End Name Score Strand 0 chr1 2110753 2111010 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpnw6anvr0/f1.bed -b /tmp/tmpnw6anvr0/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 7705642 7707393 a 0 + 1 chr1 9267901 9272722 a 0 + 2 chr1 298981 298982 a 0 - 3 chr1 6914721 6914847 a 0 - 4 chr2 8394019 8397716 a 0 + 5 chr7 4357950 4367436 a 0 + 6 chr8 7857785 7866760 a 0 + 7 chr9 9999999 10002963 a 0 + 8 chr13 4396253 4403961 a 0 - 9 chr14 9211230 9216690 a 0 + 10 chr21 6153178 6154523 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpnwed0xxl/f1.bed -b /tmp/tmpnwed0xxl/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp81lc0eo5/f1.bed -b /tmp/tmp81lc0eo5/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 2092336 2101297 a 0 + 1 chr1 8239548 8240499 a 0 + 2 chr5 7993508 7996644 a 0 + 3 chr11 348321 349390 a 0 + 4 chr14 6100831 6106654 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpssialnyn/f1.bed -b /tmp/tmpssialnyn/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp7ezvuirz/f1.bed -b /tmp/tmp7ezvuirz/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 4490717 4499509 a 0 + 1 chr1 7432293 7439158 a 0 + 2 chr1 9773390 9780091 a 0 + 3 chr1 8728508 8734129 a 0 + 4 chr1 4537042 4546212 a 0 - 5 chr5 2934271 2943537 a 0 + 6 chr7 6869995 6872973 a 0 + 7 chr12 5895302 5900279 a 0 + 8 chr12 10000000 10001630 a 0 - 9 chr18 2233684 2239985 a 0 - 10 chrX 5091581 5099926 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpzho5i74a/f1.bed -b /tmp/tmpzho5i74a/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpfx5kpymv/f1.bed -b /tmp/tmpfx5kpymv/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 9106564 9109946 a 0 - 1 chr9 1 100 a 0 - 2 chr14 9592702 9593025 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpr0fqb4po/f1.bed -b /tmp/tmpr0fqb4po/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpg2xzsdk8/f1.bed -b /tmp/tmpg2xzsdk8/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 2420380 2428478 a 0 + 1 chr1 4782868 4784388 a 0 + 2 chr1 10000000 10001646 a 0 + 3 chr1 4717338 4724940 a 0 + 4 chr1 4133418 4139223 a 0 - 5 chr1 149982 153495 a 0 - 6 chr4 1869100 1877970 a 0 - 7 chr7 3255342 3261519 a 0 - 8 chr11 1 3 a 0 + 9 chr16 5730560 5736328 a 0 + 10 chrY 2729980 2738139 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpq0rukey9/f1.bed -b /tmp/tmpq0rukey9/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmphh43oemy/f1.bed -b /tmp/tmphh43oemy/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 9156583 9157309 a 0 + 1 chr1 8996291 9002876 a 0 + 2 chr3 7634042 7643138 a 0 - 3 chr5 5058548 5058930 a 0 - 4 chr12 7658242 7662430 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpew4vmkjs/f1.bed -b /tmp/tmpew4vmkjs/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpzkl2eurq/f1.bed -b /tmp/tmpzkl2eurq/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 2105174 2108796 a 0 + 1 chr1 509891 515502 a 0 + 2 chr17 2810408 2820408 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpbqvqmecw/f1.bed -b /tmp/tmpbqvqmecw/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpvo1q1wjh/f1.bed -b /tmp/tmpvo1q1wjh/f2.bed Chromosome Start End Name Score Strand 0 chr5 1 2 a 0 + 1 chr5 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 2227131 2232412 a 0 + 1 chr1 2227131 2228169 a 0 - 2 chr18 6133039 6141533 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpsg4jt4em/f1.bed -b /tmp/tmpsg4jt4em/f2.bed Chromosome Start End Name Score Strand 0 chr5 1 2 a 0 + 1 chr5 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpeljce_91/f1.bed -b /tmp/tmpeljce_91/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 2 899 a 0 + 1 chr1 23447 33326 a 0 + 2 chr1 3016073 3025969 a 0 + 3 chr1 4949302 4956696 a 0 - 4 chr1 1744198 1748443 a 0 - 5 chr1 5009765 5018240 a 0 - 6 chr5 4537584 4542961 a 0 - 7 chr7 7179120 7189120 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpgiwbdupg/f1.bed -b /tmp/tmpgiwbdupg/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpqixocep2/f1.bed -b /tmp/tmpqixocep2/f2.bed Chromosome Start End Name Score Strand 0 chr18 1 2 a 0 + 1 chr21 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 2058647 2059600 a 0 + 1 chr1 1183565 1185879 a 0 + 2 chr1 169773 172391 a 0 + 3 chr1 115520 118138 a 0 - 4 chr1 10000000 10004489 a 0 - 5 chr1 7048806 7051424 a 0 - 6 chr6 9411540 9414158 a 0 - 7 chr11 7804461 7809337 a 0 + 8 chr15 3765505 3768123 a 0 - 9 chrY 8486850 8495884 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpz5wy878o/f1.bed -b /tmp/tmpz5wy878o/f2.bed Chromosome Start End Name Score Strand 0 chr18 1 2 a 0 + 1 chr21 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpkktqgc73/f1.bed -b /tmp/tmpkktqgc73/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1279309 1284218 a 0 - 1 chr1 1521054 1526103 a 0 - 2 chr1 2375449 2378686 a 0 - 3 chr1 8273423 8279767 a 0 - 4 chr1 8273423 8275885 a 0 - 5 chr3 8340081 8344041 a 0 - 6 chr11 6180745 6185399 a 0 - 7 chr21 3604897 3610180 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpxjw6kulh/f1.bed -b /tmp/tmpxjw6kulh/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpfuxktjdc/f1.bed -b /tmp/tmpfuxktjdc/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr22 2897300 2904273 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpw02ndzql/f1.bed -b /tmp/tmpw02ndzql/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmppq56h6yv/f1.bed -b /tmp/tmppq56h6yv/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 838553 842951 a 0 + 1 chr1 9745504 9749902 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpks9kf5p4/f1.bed -b /tmp/tmpks9kf5p4/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmphnhh29gc/f1.bed -b /tmp/tmphnhh29gc/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 4131608 4141288 a 0 + 1 chr1 3486357 3492073 a 0 + 2 chr1 5684707 5691836 a 0 + 3 chr1 9770686 9773749 a 0 + 4 chr1 3372961 3377643 a 0 - 5 chr1 5537368 5541556 a 0 - 6 chr1 5067321 5069393 a 0 - 7 chr1 7011748 7014258 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpjp2b5n4r/f1.bed -b /tmp/tmpjp2b5n4r/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmptu_6ok2q/f1.bed -b /tmp/tmptu_6ok2q/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 3809374 3811062 a 0 + 1 chr1 5357327 5361659 a 0 + 2 chr6 811195 816205 a 0 + 3 chr8 6367018 6370645 a 0 - 4 chr17 7304179 7304401 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpz6cz8d9h/f1.bed -b /tmp/tmpz6cz8d9h/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp2v8zuq_v/f1.bed -b /tmp/tmp2v8zuq_v/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 9099446 9107836 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpk8rskoi_/f1.bed -b /tmp/tmpk8rskoi_/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpa8v_2ypp/f1.bed -b /tmp/tmpa8v_2ypp/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr12 940899 949164 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpgq5nt0fp/f1.bed -b /tmp/tmpgq5nt0fp/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp9pxesdw2/f1.bed -b /tmp/tmp9pxesdw2/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr20 8513528 8519208 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpvly8lgmn/f1.bed -b /tmp/tmpvly8lgmn/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpy0886t62/f1.bed -b /tmp/tmpy0886t62/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1298363 1306063 a 0 - 1 chr10 3782147 3784333 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpwsqn3j3m/f1.bed -b /tmp/tmpwsqn3j3m/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpd6krg202/f1.bed -b /tmp/tmpd6krg202/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 4350848 4355329 a 0 + 1 chr22 4067328 4071809 a 0 - 2 chr22 9836156 9840637 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp55wyx80v/f1.bed -b /tmp/tmp55wyx80v/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpue1i7fl6/f1.bed -b /tmp/tmpue1i7fl6/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 7929066 7935243 a 0 + 1 chr1 6933800 6937448 a 0 + 2 chr1 3891381 3899131 a 0 + 3 chr1 8353623 8363623 a 0 + 4 chr1 7010783 7012228 a 0 + 5 chr1 1169991 1174462 a 0 + 6 chr1 3128698 3131854 a 0 - 7 chr5 7460709 7462195 a 0 + 8 chr14 810125 819426 a 0 - 9 chr18 9079361 9087992 a 0 + 10 chr19 6442171 6450575 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpx2bz6te3/f1.bed -b /tmp/tmpx2bz6te3/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpvzt6mwbj/f1.bed -b /tmp/tmpvzt6mwbj/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 6869155 6870614 a 0 + 1 chr1 6299203 6307908 a 0 + 2 chr1 2209069 2218599 a 0 - 3 chr1 9311721 9318184 a 0 - 4 chr1 10000000 10000001 a 0 - 5 chr6 8873098 8881454 a 0 + 6 chr9 1 4631 a 0 + 7 chr19 8572499 8576012 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpwbznf1ug/f1.bed -b /tmp/tmpwbznf1ug/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpcdc0idhs/f1.bed -b /tmp/tmpcdc0idhs/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 2006275 2011262 a 0 + 1 chr1 5072366 5077721 a 0 + 2 chr1 6950570 6959470 a 0 - 3 chr1 4275704 4278406 a 0 - 4 chr6 9737618 9742973 a 0 + 5 chr11 4729480 4737976 a 0 + 6 chr15 2 5357 a 0 + 7 chr15 824707 830062 a 0 - 8 chr18 8613514 8618869 a 0 + 9 chrY 6766230 6771585 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpq0av70v8/f1.bed -b /tmp/tmpq0av70v8/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr17 6201607 6206026 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpb6ksov3s/f1.bed -b /tmp/tmpb6ksov3s/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr2 7985489 7992579 a 0 - 1 chr9 3162250 3170064 a 0 + 2 chr16 8742035 8751967 a 0 + 3 chr19 1284666 1294598 a 0 + 4 chr20 3162250 3168047 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp8b825hq5/f1.bed -b /tmp/tmp8b825hq5/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 2894691 2894693 a 0 + 1 chr1 4485221 4494782 a 0 + 2 chr1 7185232 7195232 a 0 + 3 chr1 3024415 3026597 a 0 + 4 chr1 7953663 7960583 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpboajcz00/f1.bed -b /tmp/tmpboajcz00/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr7 3612636 3622636 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpnqktvhs8/f1.bed -b /tmp/tmpnqktvhs8/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 3623305 3633305 a 0 - 1 chr12 6810653 6818804 a 0 + 2 chr13 5682206 5689853 a 0 + 3 chr18 274761 276755 a 0 - 4 chr22 7160212 7160997 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpzbcnrcdv/f1.bed -b /tmp/tmpzbcnrcdv/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 826724 833100 a 0 + 1 chr1 1566475 1569858 a 0 - 2 chr1 1734921 1738360 a 0 - 3 chr1 9076114 9081047 a 0 - 4 chr1 10000000 10000372 a 0 - 5 chr1 4317569 4324431 a 0 - 6 chr1 2572762 2574599 a 0 - 7 chr18 9823857 9829094 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpdwlp43j8/f1.bed -b /tmp/tmpdwlp43j8/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr20 277997 280694 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpn2uapci3/f1.bed -b /tmp/tmpn2uapci3/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 5932739 5932740 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpnu5h_0ac/f1.bed -b /tmp/tmpnu5h_0ac/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1580133 1587577 a 0 + 1 chr1 233375 239912 a 0 + 2 chr1 6833706 6837028 a 0 + 3 chr1 4065818 4075817 a 0 + 4 chr1 9926384 9929000 a 0 - 5 chr6 3639076 3645017 a 0 + 6 chr7 4513044 4516568 a 0 + 7 chr8 2358345 2361349 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpjuu5n8nc/f1.bed -b /tmp/tmpjuu5n8nc/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr20 8080021 8083870 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpcrte_3a7/f1.bed -b /tmp/tmpcrte_3a7/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 9279368 9286536 a 0 + 1 chr1 5641818 5650191 a 0 + 2 chr1 6715986 6720545 a 0 + 3 chr22 7347605 7350158 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpuhna481h/f1.bed -b /tmp/tmpuhna481h/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 9271080 9271773 a 0 - 1 chr3 894813 900574 a 0 - 2 chr4 1476099 1477087 a 0 - 3 chr17 1 694 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp5n2cxlde/f1.bed -b /tmp/tmp5n2cxlde/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 5211556 5219367 a 0 - 1 chr1 10000000 10001576 a 0 - 2 chr1 9031162 9041035 a 0 - 3 chr15 3138781 3140179 a 0 + 4 chr22 5210470 5215377 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpeg2v0p9q/f1.bed -b /tmp/tmpeg2v0p9q/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr7 2661130 2667372 a 0 + 1 chr11 9381453 9388373 a 0 + 2 chr11 9381453 9383775 a 0 + 3 chr11 9381453 9390713 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpye68b047/f1.bed -b /tmp/tmpye68b047/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr6 1217229 1226721 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpxrlst_od/f1.bed -b /tmp/tmpxrlst_od/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 3413018 3416996 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp_iqmjmai/f1.bed -b /tmp/tmp_iqmjmai/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 9408896 9411320 a 0 + 1 chr1 8293792 8303428 a 0 + 2 chr1 404357 406518 a 0 + 3 chr1 6523937 6532077 a 0 - 4 chr2 6911178 6920771 a 0 + 5 chr4 6476613 6485005 a 0 + 6 chr9 4505712 4515712 a 0 - 7 chr12 4321235 4329332 a 0 - 8 chr16 8219223 8220359 a 0 + 9 chr17 905374 907694 a 0 + 10 chr17 760864 769241 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpfbks5dh_/f1.bed -b /tmp/tmpfbks5dh_/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 8954663 8963098 a 0 - 1 chr3 8640870 8641172 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpt1ounoza/f1.bed -b /tmp/tmpt1ounoza/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr17 8308 13634 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpujg2o6bb/f1.bed -b /tmp/tmpujg2o6bb/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 1042 a 0 + 1 chr1 1690596 1690657 a 0 - 2 chr1 1614058 1620837 a 0 - 3 chr1 2481296 2490390 a 0 - 4 chr9 8574134 8579713 a 0 + 5 chr9 1551978 1554498 a 0 + 6 chr9 4953680 4953834 a 0 - 7 chr14 9999999 10008715 a 0 + 8 chr16 6992005 6992007 a 0 + 9 chr16 4529500 4531248 a 0 - 10 chr18 4219999 4220412 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmple3j5wqt/f1.bed -b /tmp/tmple3j5wqt/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 9429362 9431956 a 0 + 1 chr1 8662781 8667053 a 0 - 2 chr1 2423160 2427129 a 0 - 3 chr1 4287015 4295883 a 0 - 4 chr9 7031522 7033206 a 0 + 5 chr10 7031522 7034375 a 0 + 6 chr11 7031522 7036084 a 0 + 7 chr14 1249796 1250260 a 0 + 8 chr15 1486441 1491306 a 0 + 9 chr21 2452535 2455469 a 0 + 10 chr21 7031522 7032196 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmprlzgjak_/f1.bed -b /tmp/tmprlzgjak_/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 4655561 4665560 a 0 + 1 chr1 8307672 8316794 a 0 - 2 chr2 2207549 2212676 a 0 + 3 chr11 1 9452 a 0 - 4 chr16 9701451 9710598 a 0 - 5 chr17 2920307 2921864 a 0 - 6 chr22 138443 143263 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpdsrxicaw/f1.bed -b /tmp/tmpdsrxicaw/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 6504964 6504966 a 0 + 1 chr1 3318352 3320129 a 0 + 2 chr1 850153 851642 a 0 + 3 chr1 7120795 7129462 a 0 + 4 chr5 9724579 9727851 a 0 + 5 chr17 9106807 9107473 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp03kgh9e7/f1.bed -b /tmp/tmp03kgh9e7/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 5689911 5692244 a 0 - 1 chr12 8375350 8375427 a 0 + 2 chr12 3097080 3103664 a 0 + 3 chr12 3682676 3687855 a 0 - 4 chr12 7925572 7925791 a 0 - 5 chr15 7981938 7989512 a 0 + 6 chr15 7141622 7150029 a 0 + 7 chr18 7909238 7909275 a 0 - 8 chrX 8931705 8940346 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpmmz5y85l/f1.bed -b /tmp/tmpmmz5y85l/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 3859872 3864521 a 0 + 1 chr1 3095419 3096256 a 0 - 2 chr1 7969488 7971683 a 0 - 3 chr1 7969488 7977893 a 0 - 4 chr5 4446869 4453932 a 0 + 5 chr11 7969488 7971462 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpgdh3r5rl/f1.bed -b /tmp/tmpgdh3r5rl/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr16 4070415 4076144 a 0 + 1 chr16 9341299 9351162 a 0 + 2 chr16 1353162 1360714 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp81s0630f/f1.bed -b /tmp/tmp81s0630f/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 8675971 8676386 a 0 + 1 chrX 1656521 1663075 a 0 + 2 chrX 3169938 3175182 a 0 - 3 chrX 2436587 2444939 a 0 - 4 chrX 5605598 5607909 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpcgzgecoq/f1.bed -b /tmp/tmpcgzgecoq/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 10000000 10000415 a 0 + 1 chr1 8435956 8440774 a 0 - 2 chr4 418234 420724 a 0 + 3 chr22 6842251 6845197 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp6ds747mx/f1.bed -b /tmp/tmp6ds747mx/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 6955135 6960128 a 0 + 1 chr1 8553318 8559287 a 0 + 2 chr1 6955135 6962712 a 0 + 3 chr1 6955135 6960128 a 0 + 4 chr1 6955135 6959280 a 0 + 5 chr1 6955135 6960284 a 0 - 6 chr1 8332341 8340499 a 0 - 7 chr19 10000000 10007635 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp_41usklk/f1.bed -b /tmp/tmp_41usklk/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr13 452495 462414 a 0 - 1 chr15 2117551 2118653 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp7bbgdzjz/f1.bed -b /tmp/tmp7bbgdzjz/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 4254681 4261520 a 0 + 1 chr1 775402 784655 a 0 - 2 chr5 299625 308664 a 0 - 3 chr7 4545379 4554418 a 0 - 4 chr13 8284044 8292633 a 0 + 5 chr13 3568302 3569752 a 0 + 6 chr18 9098981 9103118 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpf3meop0f/f1.bed -b /tmp/tmpf3meop0f/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 8507464 8508401 a 0 + 1 chr1 9227305 9233054 a 0 + 2 chr1 1603725 1608443 a 0 + 3 chr1 6324621 6333832 a 0 + 4 chr1 9985059 9991314 a 0 - 5 chr1 3770146 3774016 a 0 - 6 chr1 5238343 5245155 a 0 - 7 chr1 4795867 4805023 a 0 - 8 chr5 1255257 1262069 a 0 + 9 chr9 1657480 1661734 a 0 - 10 chrM 1109625 1110398 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpjn0zsixk/f1.bed -b /tmp/tmpjn0zsixk/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 5438616 5442804 a 0 + 1 chr1 2284703 2288891 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp41f1xufq/f1.bed -b /tmp/tmp41f1xufq/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1500837 1505480 a 0 + 1 chr1 4957594 4963582 a 0 + 2 chr1 4957594 4965803 a 0 + 3 chr1 2304136 2309484 a 0 + 4 chr1 1105347 1115147 a 0 + 5 chr1 4957594 4963437 a 0 + 6 chr16 7326452 7332715 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpwfni1fu5/f1.bed -b /tmp/tmpwfni1fu5/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 5664534 5673605 a 0 + 1 chr1 1699081 1705492 a 0 + 2 chr13 585574 591071 a 0 + 3 chr13 7253514 7260005 a 0 - 4 chr16 8928884 8938267 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpdfw1hjnu/f1.bed -b /tmp/tmpdfw1hjnu/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr12 5722108 5724892 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpzfalz21n/f1.bed -b /tmp/tmpzfalz21n/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 5402140 5402594 a 0 + 1 chr1 1 9850 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpem7mty46/f1.bed -b /tmp/tmpem7mty46/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 4148655 4157819 a 0 + 1 chr1 4148655 4154907 a 0 - 2 chr1 2318462 2327626 a 0 - 3 chr5 4445506 4447890 a 0 + 4 chr6 4145298 4152516 a 0 - 5 chr9 9463967 9472014 a 0 - 6 chr12 4366553 4375717 a 0 - 7 chr12 1803242 1808690 a 0 - 8 chr13 4148655 4157819 a 0 - 9 chr14 3839672 3843110 a 0 - 10 chr17 3685357 3695080 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmps485a2pd/f1.bed -b /tmp/tmps485a2pd/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 9629646 9635846 a 0 + 1 chr1 4852733 4859418 a 0 + 2 chr5 8566531 8573961 a 0 + 3 chr6 9100860 9108302 a 0 + 4 chr9 6827084 6832096 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp8tgtusfd/f1.bed -b /tmp/tmp8tgtusfd/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1403159 1405998 a 0 + 1 chr1 1924141 1930812 a 0 + 2 chr1 2506743 2510795 a 0 + 3 chr1 9852236 9854286 a 0 - 4 chr6 5078174 5079512 a 0 - 5 chr10 10000000 10009938 a 0 - 6 chr17 274640 277585 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpliuw1bwf/f1.bed -b /tmp/tmpliuw1bwf/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 4174198 4179290 a 0 + 1 chr1 4324774 4327626 a 0 - 2 chr1 7151996 7153799 a 0 - 3 chr1 3244549 3249498 a 0 - 4 chr1 8910591 8914590 a 0 - 5 chr1 5034530 5041627 a 0 - 6 chr5 8278923 8281441 a 0 + 7 chr10 7556290 7557147 a 0 + 8 chr10 5496023 5506022 a 0 - 9 chr20 9162189 9171927 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmptu23ckeb/f1.bed -b /tmp/tmptu23ckeb/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 9236403 9236404 a 0 + 1 chr1 3211396 3212976 a 0 + 2 chr1 1735328 1740033 a 0 + 3 chr1 10000000 10000001 a 0 - 4 chr1 7008611 7018591 a 0 - 5 chr1 9236403 9245197 a 0 - 6 chr8 7069160 7076480 a 0 + 7 chr10 1382877 1386670 a 0 - 8 chr12 9236403 9245829 a 0 - 9 chr13 1166345 1168397 a 0 - 10 chr14 5996645 5996646 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp464n85o2/f1.bed -b /tmp/tmp464n85o2/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 9821383 9831168 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp46n5hrpq/f1.bed -b /tmp/tmp46n5hrpq/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr20 5835172 5837545 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpkr0j8a_k/f1.bed -b /tmp/tmpkr0j8a_k/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 2424360 2431452 a 0 + 1 chr1 5953639 5953640 a 0 - 2 chr5 10000000 10009295 a 0 - 3 chr8 8867672 8872742 a 0 - 4 chr11 9558451 9567319 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmprjpcjajt/f1.bed -b /tmp/tmprjpcjajt/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 4135168 4142330 a 0 - 1 chr1 3859433 3868125 a 0 - 2 chrX 2869120 2876282 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpov_o86uw/f1.bed -b /tmp/tmpov_o86uw/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 9874505 9882667 a 0 + 1 chr1 5834341 5842503 a 0 + 2 chr1 9290182 9298344 a 0 + 3 chr20 4618388 4626550 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp4op48nu9/f1.bed -b /tmp/tmp4op48nu9/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 2928812 2933040 a 0 + 1 chr1 675297 685297 a 0 - 2 chr4 3174369 3183050 a 0 + 3 chr11 4284031 4287587 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpmq6fx_a6/f1.bed -b /tmp/tmpmq6fx_a6/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1703285 1703801 a 0 - 1 chr1 9272773 9276942 a 0 - 2 chr1 5201495 5206046 a 0 - 3 chr1 4863094 4867573 a 0 - 4 chr13 1286478 1290647 a 0 - 5 chr14 2519371 2523540 a 0 - 6 chr16 6019003 6026336 a 0 - 7 chr17 3981989 3988854 a 0 - 8 chr20 4849217 4851127 a 0 - 9 chrX 3435995 3440164 a 0 - 10 chrX 6273326 6280235 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpu2guvjo2/f1.bed -b /tmp/tmpu2guvjo2/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 3395637 3397462 a 0 - 1 chr9 6540602 6546843 a 0 + 2 chr9 2885162 2894923 a 0 + 3 chr9 631241 631803 a 0 - 4 chr9 367948 373778 a 0 - 5 chr9 3875980 3881676 a 0 - 6 chr12 3291003 3297972 a 0 - 7 chr15 4606240 4610790 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpbvkwtlba/f1.bed -b /tmp/tmpbvkwtlba/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 10000000 10009934 a 0 - 1 chr9 10000000 10000002 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpx8qd73p8/f1.bed -b /tmp/tmpx8qd73p8/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 260820 268903 a 0 + 1 chr1 260820 268418 a 0 + 2 chr1 260820 263554 a 0 + 3 chr1 260820 265642 a 0 - 4 chr2 5020355 5028701 a 0 + 5 chr2 6524824 6526167 a 0 - 6 chr15 260820 263101 a 0 + 7 chr15 260820 270266 a 0 - 8 chr16 2541808 2548167 a 0 - 9 chr20 10000000 10008528 a 0 - 10 chrM 260820 261206 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpjhi8y8vb/f1.bed -b /tmp/tmpjhi8y8vb/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 2 4191 a 0 + 1 chr1 5157263 5161452 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp57tbgpg8/f1.bed -b /tmp/tmp57tbgpg8/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 4117095 4120338 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp360ewlto/f1.bed -b /tmp/tmp360ewlto/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1293990 1303703 a 0 + 1 chr1 8775574 8784346 a 0 + 2 chr1 1486399 1494498 a 0 + 3 chr1 7904536 7909820 a 0 + 4 chr1 2504093 2504818 a 0 - 5 chr20 5373713 5377549 a 0 - 6 chrM 5373713 5381147 a 0 - 7 chrY 442468 446964 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmptczelw1p/f1.bed -b /tmp/tmptczelw1p/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 3391791 3394579 a 0 + 1 chr1 3391791 3395030 a 0 - 2 chr1 3391791 3397722 a 0 - 3 chr1 3391791 3401791 a 0 - 4 chr1 3391791 3399824 a 0 - 5 chr1 3391791 3397314 a 0 - 6 chr1 3391791 3397359 a 0 - 7 chr2 3391791 3396836 a 0 - 8 chr2 7745894 7751427 a 0 - 9 chr3 3391791 3399613 a 0 - 10 chr18 3391791 3395325 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp4_229n3n/f1.bed -b /tmp/tmp4_229n3n/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 2039846 2046362 a 0 + 1 chr1 6364313 6370460 a 0 + 2 chr1 9014156 9017569 a 0 + 3 chr1 7956649 7960631 a 0 + 4 chr1 5234602 5238015 a 0 + 5 chr1 3107360 3116536 a 0 - 6 chr1 2779273 2780507 a 0 - 7 chr8 8728571 8729855 a 0 - 8 chr8 263279 266692 a 0 - 9 chr22 7956649 7959898 a 0 + 10 chrX 631804 635780 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpt47yuy0_/f1.bed -b /tmp/tmpt47yuy0_/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr6 191809 194611 a 0 - 1 chr8 7253083 7257873 a 0 + 2 chr8 8288052 8295289 a 0 - 3 chr8 9883212 9889396 a 0 - 4 chr8 6939228 6947052 a 0 - 5 chr9 125886 134764 a 0 + 6 chr11 8008525 8013696 a 0 + 7 chr11 1188777 1197901 a 0 + 8 chr14 8488573 8497422 a 0 + 9 chr20 2587582 2588085 a 0 + 10 chr21 8118387 8118890 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp2xs2xs6r/f1.bed -b /tmp/tmp2xs2xs6r/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 9616369 9617313 a 0 - 1 chr7 4006466 4010472 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmps1h0h6w8/f1.bed -b /tmp/tmps1h0h6w8/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr15 5364110 5367454 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpqa482pdt/f1.bed -b /tmp/tmpqa482pdt/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 5671379 5676696 a 0 + 1 chr1 3812384 3814512 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpt0izwu1g/f1.bed -b /tmp/tmpt0izwu1g/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr11 1608268 1612406 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpa8rayqx4/f1.bed -b /tmp/tmpa8rayqx4/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr5 9999999 10008564 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpup8z97sd/f1.bed -b /tmp/tmpup8z97sd/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 9093939 9103938 a 0 + 1 chr1 3510469 3511303 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpgeie0nb8/f1.bed -b /tmp/tmpgeie0nb8/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 10000000 10002501 a 0 - 1 chr5 1597676 1606557 a 0 - 2 chr15 7249600 7252313 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmprhb6uong/f1.bed -b /tmp/tmprhb6uong/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 7318683 7320061 a 0 + 1 chr17 10000000 10008657 a 0 + 2 chr21 6321194 6328392 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmplwfmabo1/f1.bed -b /tmp/tmplwfmabo1/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 576893 579977 a 0 - 1 chr1 8082013 8088197 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmph70nszia/f1.bed -b /tmp/tmph70nszia/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 9742003 9744210 a 0 + 1 chr1 8863820 8867835 a 0 - 2 chr1 7847277 7857119 a 0 - 3 chr1 1926722 1933313 a 0 - 4 chr4 1926722 1928929 a 0 - 5 chr12 62956 71594 a 0 - 6 chr12 9906803 9912709 a 0 - 7 chr14 7638643 7645126 a 0 - 8 chr20 1926722 1928929 a 0 - 9 chr20 2288372 2290879 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpw13__7cn/f1.bed -b /tmp/tmpw13__7cn/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 8331650 8341034 a 0 + 1 chr1 1980357 1984633 a 0 + 2 chr1 9402266 9402492 a 0 + 3 chr1 5919545 5926412 a 0 - 4 chr1 2299816 2309625 a 0 - 5 chr1 5919545 5922995 a 0 - 6 chr1 5349389 5356825 a 0 - 7 chr1 2741191 2748278 a 0 - 8 chr4 3979677 3986764 a 0 + 9 chr6 7173782 7176979 a 0 + 10 chr14 8054152 8062644 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpl7hr_bmh/f1.bed -b /tmp/tmpl7hr_bmh/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 9117096 9125564 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpewslb1bm/f1.bed -b /tmp/tmpewslb1bm/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 4177071 4187028 a 0 + 1 chr1 559817 560372 a 0 - 2 chr1 8935456 8939029 a 0 - 3 chr3 7232941 7232942 a 0 + 4 chr5 3324537 3327531 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpx5769sum/f1.bed -b /tmp/tmpx5769sum/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 2170120 2170867 a 0 + 1 chr1 9217254 9226042 a 0 + 2 chr1 1708697 1709809 a 0 + 3 chr1 3929810 3937082 a 0 - 4 chr1 8498774 8499892 a 0 - 5 chr1 3987143 3993489 a 0 - 6 chr13 9217254 9222579 a 0 - 7 chr15 593404 599845 a 0 - 8 chr22 9771936 9780284 a 0 - 9 chrX 8331425 8339658 a 0 - 10 chrY 9217254 9226756 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmprd7j7i9t/f1.bed -b /tmp/tmprd7j7i9t/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr7 3667497 3670328 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpru386z9f/f1.bed -b /tmp/tmpru386z9f/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 4094320 4100594 a 0 + 1 chr1 9629794 9639712 a 0 + 2 chr1 9577664 9585048 a 0 + 3 chr1 9999999 10005765 a 0 + 4 chr8 1464803 1472073 a 0 - 5 chr9 3071837 3072612 a 0 - 6 chr10 5168921 5174304 a 0 - 7 chr12 2131419 2134331 a 0 - 8 chr17 7753730 7756198 a 0 + 9 chr20 4008748 4018062 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp3motnzbj/f1.bed -b /tmp/tmp3motnzbj/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 6585193 6593133 a 0 - 1 chr1 6585193 6588112 a 0 - 2 chr12 6900851 6903770 a 0 + 3 chr19 4875790 4878709 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmprrtgynnd/f1.bed -b /tmp/tmprrtgynnd/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 7014 a 0 + 1 chr1 5261811 5268824 a 0 + 2 chr1 3953280 3960293 a 0 - 3 chr6 5780082 5787095 a 0 + 4 chr8 3045623 3052636 a 0 + 5 chr16 9609987 9617000 a 0 + 6 chr21 8247007 8252784 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpuz62o30q/f1.bed -b /tmp/tmpuz62o30q/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1703122 1712458 a 0 + 1 chr1 1584971 1592570 a 0 - 2 chr1 2812178 2821417 a 0 - 3 chr6 571376 580088 a 0 - 4 chr8 1056909 1061613 a 0 - 5 chr10 6462711 6467556 a 0 - 6 chr11 3763078 3770719 a 0 - 7 chr13 10000000 10000052 a 0 + 8 chr13 8468935 8474338 a 0 - 9 chr18 1807911 1813496 a 0 - 10 chr21 8917051 8919117 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpxpx04vcz/f1.bed -b /tmp/tmpxpx04vcz/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1319746 1324351 a 0 + 1 chr1 21545 22035 a 0 + 2 chr1 9999999 10009025 a 0 + 3 chr16 2485495 2490100 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp6dllvr88/f1.bed -b /tmp/tmp6dllvr88/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 4705171 4705172 a 0 + 1 chr9 2043554 2045353 a 0 - 2 chr11 6130442 6133670 a 0 + 3 chr13 7302948 7309958 a 0 - 4 chr17 8726017 8729222 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpyg6xfmip/f1.bed -b /tmp/tmpyg6xfmip/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 2554615 2560201 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp2rqanq2r/f1.bed -b /tmp/tmp2rqanq2r/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 9690304 9698606 a 0 - 1 chr21 6432434 6438094 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpe6dq1hkv/f1.bed -b /tmp/tmpe6dq1hkv/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 8033669 8036399 a 0 + 1 chr1 8044661 8054473 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpkyqala_3/f1.bed -b /tmp/tmpkyqala_3/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 4166936 4169858 a 0 + 1 chr5 7999788 8005064 a 0 - 2 chr11 6779689 6786242 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpiahx2t54/f1.bed -b /tmp/tmpiahx2t54/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 2041735 2050408 a 0 + 1 chr1 8854746 8859283 a 0 + 2 chr1 6934409 6943082 a 0 + 3 chr1 5296281 5304954 a 0 + 4 chr1 2102565 2111238 a 0 + 5 chr1 7185173 7193846 a 0 - 6 chr1 2490881 2499554 a 0 - 7 chr1 1346102 1354775 a 0 - 8 chr4 9895305 9903978 a 0 + 9 chr16 3214750 3215714 a 0 + 10 chrX 6559251 6568879 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpxpscunue/f1.bed -b /tmp/tmpxpscunue/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 3320920 3321875 a 0 + 1 chr1 6482787 6489433 a 0 + 2 chr1 3151090 3156404 a 0 - 3 chr15 8583629 8589916 a 0 - 4 chr19 1639623 1646843 a 0 - 5 chrX 4395328 4396268 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpbloezg63/f1.bed -b /tmp/tmpbloezg63/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 2259655 2261525 a 0 + 1 chr1 266352 268652 a 0 - 2 chr1 556251 558642 a 0 - 3 chr1 3005493 3011287 a 0 - 4 chr15 37780 47709 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp8bfyvn3h/f1.bed -b /tmp/tmp8bfyvn3h/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 3082188 3086695 a 0 + 1 chr1 8046848 8052408 a 0 - 2 chr11 9049105 9052003 a 0 - 3 chr17 1848094 1857691 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpk8he1m19/f1.bed -b /tmp/tmpk8he1m19/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr6 6076976 6084347 a 0 - 1 chr10 9205465 9205466 a 0 + 2 chr16 7804583 7806526 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpqy8im326/f1.bed -b /tmp/tmpqy8im326/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 4592302 4599145 a 0 - 1 chr1 10000000 10009829 a 0 - 2 chr1 8333358 8339338 a 0 - 3 chr14 1415918 1421748 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpcwtnz4t2/f1.bed -b /tmp/tmpcwtnz4t2/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 6586818 6596147 a 0 + 1 chr1 5258996 5262860 a 0 + 2 chr1 3475489 3478684 a 0 + 3 chr1 7327441 7335078 a 0 + 4 chr1 3827327 3832826 a 0 + 5 chr1 2 9561 a 0 - 6 chr1 9789626 9790578 a 0 - 7 chr1 704465 713094 a 0 - 8 chr11 8995811 8998948 a 0 + 9 chr15 1106109 1112533 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpuabgxxx8/f1.bed -b /tmp/tmpuabgxxx8/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr2 4470948 4471824 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmptoxjwx6_/f1.bed -b /tmp/tmptoxjwx6_/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 7100011 7105671 a 0 + 1 chr1 6570395 6571521 a 0 + 2 chr1 10000000 10004206 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpctl0inlk/f1.bed -b /tmp/tmpctl0inlk/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 4240252 4241589 a 0 + 1 chr1 4441370 4448185 a 0 - 2 chr12 4441370 4442606 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp6tblgruh/f1.bed -b /tmp/tmp6tblgruh/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 2024333 2031832 a 0 + 1 chr1 8394531 8396535 a 0 + 2 chr1 1089325 1097009 a 0 - 3 chr5 1089325 1098736 a 0 + 4 chr10 1089325 1097533 a 0 - 5 chr11 1089325 1095491 a 0 + 6 chr12 1089325 1099325 a 0 + 7 chr17 1089325 1099308 a 0 + 8 chr17 1089325 1090090 a 0 - 9 chr19 1089325 1093680 a 0 + 10 chrY 1089325 1096571 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpql3l75q3/f1.bed -b /tmp/tmpql3l75q3/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr14 1561851 1563315 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp7tyjzj0y/f1.bed -b /tmp/tmp7tyjzj0y/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 4392335 4393179 a 0 + 1 chr1 6947669 6957407 a 0 + 2 chr1 4392335 4400766 a 0 + 3 chr1 4392335 4399979 a 0 - 4 chr1 4392335 4399639 a 0 - 5 chr12 4392335 4394857 a 0 + 6 chr15 8033716 8034940 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpjjaeeib7/f1.bed -b /tmp/tmpjjaeeib7/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 5592482 5593310 a 0 + 1 chr1 7576195 7580195 a 0 - 2 chr18 5592482 5602199 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpl8nmnwd5/f1.bed -b /tmp/tmpl8nmnwd5/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 2421101 2422032 a 0 + 1 chr1 4883613 4891454 a 0 + 2 chr1 3991715 3996835 a 0 + 3 chr1 1272792 1281146 a 0 + 4 chr1 8621054 8626174 a 0 - 5 chr5 4785427 4791284 a 0 + 6 chr5 4782294 4787414 a 0 + 7 chr6 1184266 1191631 a 0 + 8 chr8 1 5121 a 0 + 9 chr11 1235498 1240618 a 0 + 10 chr14 1620516 1630490 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp2tolf1di/f1.bed -b /tmp/tmp2tolf1di/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1749450 1757475 a 0 + 1 chr1 1749450 1759203 a 0 + 2 chr1 7119715 7124561 a 0 + 3 chr1 3244739 3245041 a 0 + 4 chr1 7787015 7787017 a 0 + 5 chr1 1749450 1757475 a 0 + 6 chr1 4094819 4102844 a 0 - 7 chr1 869346 877157 a 0 - 8 chr12 9542319 9552319 a 0 + 9 chr18 1125496 1128019 a 0 + 10 chrY 1749450 1751174 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp8s6tiwle/f1.bed -b /tmp/tmp8s6tiwle/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr2 7985489 7992579 a 0 - 1 chr9 3162250 3170064 a 0 + 2 chr16 8742035 8751967 a 0 + 3 chr19 1284666 1294598 a 0 + 4 chr20 3162250 3168047 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpr0bxek43/f1.bed -b /tmp/tmpr0bxek43/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 4240252 4241589 a 0 + 1 chr1 4441370 4448185 a 0 - 2 chr12 4441370 4442606 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp9arq9cpp/f1.bed -b /tmp/tmp9arq9cpp/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 6955135 6960128 a 0 + 1 chr1 8553318 8559287 a 0 + 2 chr1 6955135 6962712 a 0 + 3 chr1 6955135 6960128 a 0 + 4 chr1 6955135 6959280 a 0 + 5 chr1 6955135 6960284 a 0 - 6 chr1 8332341 8340499 a 0 - 7 chr19 10000000 10007635 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpwszef8f9/f1.bed -b /tmp/tmpwszef8f9/f2.bed Chromosome Start End Name Score Strand 0 chr1 2121401 2121658 a 0 + Chromosome Start End Name Score Strand 0 chr1 5402140 5402594 a 0 + 1 chr1 1 9850 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp_ne4ts3m/f1.bed -b /tmp/tmp_ne4ts3m/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr2 7985489 7992579 a 0 - 1 chr9 3162250 3170064 a 0 + 2 chr16 8742035 8751967 a 0 + 3 chr19 1284666 1294598 a 0 + 4 chr20 3162250 3168047 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp4grp4xuq/f1.bed -b /tmp/tmp4grp4xuq/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1293990 1303703 a 0 + 1 chr1 8775574 8784346 a 0 + 2 chr1 1486399 1494498 a 0 + 3 chr1 7904536 7909820 a 0 + 4 chr1 2504093 2504818 a 0 - 5 chr20 5373713 5377549 a 0 - 6 chrM 5373713 5381147 a 0 - 7 chrY 442468 446964 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpjdrbmsmh/f1.bed -b /tmp/tmpjdrbmsmh/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 3082188 3086695 a 0 + 1 chr1 8046848 8052408 a 0 - 2 chr11 9049105 9052003 a 0 - 3 chr17 1848094 1857691 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpxsqimg4b/f1.bed -b /tmp/tmpxsqimg4b/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 2170120 2170867 a 0 + 1 chr1 9217254 9226042 a 0 + 2 chr1 1708697 1709809 a 0 + 3 chr1 3929810 3937082 a 0 - 4 chr1 8498774 8499892 a 0 - 5 chr1 3987143 3993489 a 0 - 6 chr13 9217254 9222579 a 0 - 7 chr15 593404 599845 a 0 - 8 chr22 9771936 9780284 a 0 - 9 chrX 8331425 8339658 a 0 - 10 chrY 9217254 9226756 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpmalsvrwt/f1.bed -b /tmp/tmpmalsvrwt/f2.bed Chromosome Start End Name Score Strand 0 chr1 8198369 8198370 a 0 + Chromosome Start End Name Score Strand 0 chr1 9429362 9431956 a 0 + 1 chr1 8662781 8667053 a 0 - 2 chr1 2423160 2427129 a 0 - 3 chr1 4287015 4295883 a 0 - 4 chr9 7031522 7033206 a 0 + 5 chr10 7031522 7034375 a 0 + 6 chr11 7031522 7036084 a 0 + 7 chr14 1249796 1250260 a 0 + 8 chr15 1486441 1491306 a 0 + 9 chr21 2452535 2455469 a 0 + 10 chr21 7031522 7032196 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp0_rpgwq6/f1.bed -b /tmp/tmp0_rpgwq6/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 8033669 8036399 a 0 + 1 chr1 8044661 8054473 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpfzkhnn3e/f1.bed -b /tmp/tmpfzkhnn3e/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 7318683 7320061 a 0 + 1 chr17 10000000 10008657 a 0 + 2 chr21 6321194 6328392 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp_xlrbrz8/f1.bed -b /tmp/tmp_xlrbrz8/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 2894691 2894693 a 0 + 1 chr1 4485221 4494782 a 0 + 2 chr1 7185232 7195232 a 0 + 3 chr1 3024415 3026597 a 0 + 4 chr1 7953663 7960583 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpk6kdsq7n/f1.bed -b /tmp/tmpk6kdsq7n/f2.bed Chromosome Start End Name Score Strand 0 chr1 2121401 2121658 a 0 + Chromosome Start End Name Score Strand 0 chr1 2894691 2894693 a 0 + 1 chr1 4485221 4494782 a 0 + 2 chr1 7185232 7195232 a 0 + 3 chr1 3024415 3026597 a 0 + 4 chr1 7953663 7960583 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpzwkpxxib/f1.bed -b /tmp/tmpzwkpxxib/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 2554615 2560201 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmptompoire/f1.bed -b /tmp/tmptompoire/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr11 1608268 1612406 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpz31wut4b/f1.bed -b /tmp/tmpz31wut4b/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 5592482 5593310 a 0 + 1 chr1 7576195 7580195 a 0 - 2 chr18 5592482 5602199 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmptzisvjvu/f1.bed -b /tmp/tmptzisvjvu/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1319746 1324351 a 0 + 1 chr1 21545 22035 a 0 + 2 chr1 9999999 10009025 a 0 + 3 chr16 2485495 2490100 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpsiucscce/f1.bed -b /tmp/tmpsiucscce/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 6585193 6593133 a 0 - 1 chr1 6585193 6588112 a 0 - 2 chr12 6900851 6903770 a 0 + 3 chr19 4875790 4878709 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmppd4ftvul/f1.bed -b /tmp/tmppd4ftvul/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr16 4070415 4076144 a 0 + 1 chr16 9341299 9351162 a 0 + 2 chr16 1353162 1360714 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpj3x64ejx/f1.bed -b /tmp/tmpj3x64ejx/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 10000000 10002501 a 0 - 1 chr5 1597676 1606557 a 0 - 2 chr15 7249600 7252313 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpw2nwzj_b/f1.bed -b /tmp/tmpw2nwzj_b/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 10000000 10000415 a 0 + 1 chr1 8435956 8440774 a 0 - 2 chr4 418234 420724 a 0 + 3 chr22 6842251 6845197 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpxhywiw8v/f1.bed -b /tmp/tmpxhywiw8v/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 4177071 4187028 a 0 + 1 chr1 559817 560372 a 0 - 2 chr1 8935456 8939029 a 0 - 3 chr3 7232941 7232942 a 0 + 4 chr5 3324537 3327531 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmptjpjri4m/f1.bed -b /tmp/tmptjpjri4m/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 2006275 2011262 a 0 + 1 chr1 5072366 5077721 a 0 + 2 chr1 6950570 6959470 a 0 - 3 chr1 4275704 4278406 a 0 - 4 chr6 9737618 9742973 a 0 + 5 chr11 4729480 4737976 a 0 + 6 chr15 2 5357 a 0 + 7 chr15 824707 830062 a 0 - 8 chr18 8613514 8618869 a 0 + 9 chrY 6766230 6771585 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpce6eqccz/f1.bed -b /tmp/tmpce6eqccz/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 9279368 9286536 a 0 + 1 chr1 5641818 5650191 a 0 + 2 chr1 6715986 6720545 a 0 + 3 chr22 7347605 7350158 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpi32825xb/f1.bed -b /tmp/tmpi32825xb/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 9874505 9882667 a 0 + 1 chr1 5834341 5842503 a 0 + 2 chr1 9290182 9298344 a 0 + 3 chr20 4618388 4626550 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpl1ck2dru/f1.bed -b /tmp/tmpl1ck2dru/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 6586818 6596147 a 0 + 1 chr1 5258996 5262860 a 0 + 2 chr1 3475489 3478684 a 0 + 3 chr1 7327441 7335078 a 0 + 4 chr1 3827327 3832826 a 0 + 5 chr1 2 9561 a 0 - 6 chr1 9789626 9790578 a 0 - 7 chr1 704465 713094 a 0 - 8 chr11 8995811 8998948 a 0 + 9 chr15 1106109 1112533 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp37e_ucif/f1.bed -b /tmp/tmp37e_ucif/f2.bed Chromosome Start End Name Score Strand 0 chrX 8978951 8978952 a 0 + Chromosome Start End Name Score Strand 0 chr1 3391791 3394579 a 0 + 1 chr1 3391791 3395030 a 0 - 2 chr1 3391791 3397722 a 0 - 3 chr1 3391791 3401791 a 0 - 4 chr1 3391791 3399824 a 0 - 5 chr1 3391791 3397314 a 0 - 6 chr1 3391791 3397359 a 0 - 7 chr2 3391791 3396836 a 0 - 8 chr2 7745894 7751427 a 0 - 9 chr3 3391791 3399613 a 0 - 10 chr18 3391791 3395325 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp4j3b8trw/f1.bed -b /tmp/tmp4j3b8trw/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 9271080 9271773 a 0 - 1 chr3 894813 900574 a 0 - 2 chr4 1476099 1477087 a 0 - 3 chr17 1 694 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp4h_c0n3w/f1.bed -b /tmp/tmp4h_c0n3w/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 5592482 5593310 a 0 + 1 chr1 7576195 7580195 a 0 - 2 chr18 5592482 5602199 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpff3anq7e/f1.bed -b /tmp/tmpff3anq7e/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 9279368 9286536 a 0 + 1 chr1 5641818 5650191 a 0 + 2 chr1 6715986 6720545 a 0 + 3 chr22 7347605 7350158 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpk14adcgs/f1.bed -b /tmp/tmpk14adcgs/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpikxkebj_/f1.bed -b /tmp/tmpikxkebj_/f2.bed ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain31-method_chain31] ___________ [gw8] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', False), method_chain = ('intersect', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:292: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('intersect', 'nearest'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:110 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E (and 30 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2QAAkYwBkIgYIADRhSCEcpmYMSUR2UDAAPhABM=') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain56-method_chain56] ___________ [gw9] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', 'same') method_chain = ('set_intersect', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('set_intersect', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E /usr/lib/python3/dist-packages/natsort/utils.py:344 E (and 119 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2A0tqjUcud5xcjAyIAJADpqAk8=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') _________________ test_k_nearest[upstream-True-opposite-last] __________________ [gw4] linux -- Python 3.12.6 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 880, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 510, in test_k_nearest | @pytest.mark.explore | ^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1722, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 548, in test_k_nearest | result = gr.k_nearest( | ^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2450, in k_nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 180, in _nearest | df = __nearest(d1, d2, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 140, in nearest_next | lidx, ridx, dist = nearest_next_idx(d1, d2, d1.__k__.values, ties) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 56, in nearest_next_idx | lidx, ridx_pos, dist = k_nearest_next_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/k_nearest.pyx", line 55, in sorted_nearest.src.k_nearest.k_nearest_next_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_k_nearest( | nearest_how='upstream', | overlap=True, | strandedness='opposite', | ties='last', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:160 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:171 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:41 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:42 | (and 41 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2QAA0YGOGBkxBBiAAAAngAG') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 548, in test_k_nearest | result = gr.k_nearest( | ^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2450, in k_nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 180, in _nearest | df = __nearest(d1, d2, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 115, in nearest_previous | lidx, ridx, dist = nearest_previous_idx(d1, d2, d1.__k__.values, ties) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 28, in nearest_previous_idx | lidx, ridx_pos, dist = k_nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/k_nearest.pyx", line 28, in sorted_nearest.src.k_nearest.k_nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_k_nearest( | nearest_how='upstream', | overlap=True, | strandedness='opposite', | ties='last', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:14 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:15 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:160 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:171 | (and 40 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2QAA0YGBGDEEGIEAACLAAY=') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfe1dpknu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfe1dpknu/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpath8p76p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpath8p76p/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2iyi8uqs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2iyi8uqs/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkrh_n4gp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkrh_n4gp/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpislw26xw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpislw26xw/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmps5h6mmsp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps5h6mmsp/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp61whiebv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp61whiebv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvnyj5r0_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvnyj5r0_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmphy90wyea/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphy90wyea/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4os_d5n5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4os_d5n5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmphndux9hw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphndux9hw/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpphin4cit/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpphin4cit/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1nej3yi2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1nej3yi2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1a8tmvz8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1a8tmvz8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwjfenmgu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwjfenmgu/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcuu6_c3b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcuu6_c3b/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpamhnnnxr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpamhnnnxr/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpif452ufn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpif452ufn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnnav3fdj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnnav3fdj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmptk2eipbg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptk2eipbg/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9w0okab9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9w0okab9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqjxe95ak/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqjxe95ak/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpm59qfmae/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm59qfmae/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3klay8_f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3klay8_f/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnkb2e6ua/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnkb2e6ua/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjqy6y2k3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjqy6y2k3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3onrcyis/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3onrcyis/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp86olyyng/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp86olyyng/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuu_9ygt_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuu_9ygt_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpz5omag23/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz5omag23/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpenbqt2bo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpenbqt2bo/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5uyfr2uo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5uyfr2uo/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4mxyyaem/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4mxyyaem/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0y9966ai/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0y9966ai/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp38sg_jtv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp38sg_jtv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmte0a8nx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmte0a8nx/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnmthh6en/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnmthh6en/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpp0ohliz2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp0ohliz2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnvxbq4ug/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnvxbq4ug/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgel532cq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgel532cq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpiixax9b4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiixax9b4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmptd08ij0y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptd08ij0y/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3hqjhnmg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3hqjhnmg/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpr5xcuvkn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr5xcuvkn/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsr4yrys1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsr4yrys1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpykrto8nd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpykrto8nd/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp58i97ss9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp58i97ss9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmd8cejw8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmd8cejw8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp61ur0lxk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp61ur0lxk/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7o6j6paa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7o6j6paa/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpn4wpbugf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn4wpbugf/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpn3wkrxn8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn3wkrxn8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpj7zjd94r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj7zjd94r/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp54kercxf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp54kercxf/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpboyq_e6m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpboyq_e6m/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsh81v_mm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsh81v_mm/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmphlyuicp0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphlyuicp0/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyt6o0lg7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyt6o0lg7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgg7xxns4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgg7xxns4/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjfz3gqbo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjfz3gqbo/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpe622wc77/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe622wc77/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpt9c3l84g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt9c3l84g/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpoz6cwyn7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoz6cwyn7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxmhr1kud/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxmhr1kud/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpy0ek747f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy0ek747f/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdj2_mprt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdj2_mprt/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwvnzqxim/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwvnzqxim/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpanfthpni/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpanfthpni/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyaravwx2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyaravwx2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9otdwon8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9otdwon8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpg4gsdk2n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg4gsdk2n/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdhexlm3m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdhexlm3m/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpieofpe_g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpieofpe_g/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9zxs8k0b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9zxs8k0b/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpiyuu4g78/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiyuu4g78/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxo9_n2dj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxo9_n2dj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpp4pcdspy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp4pcdspy/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp39c8e0dh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp39c8e0dh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpf_elk16z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf_elk16z/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpq0u3r6ha/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq0u3r6ha/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqfvmyk91/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqfvmyk91/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzgrftypn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzgrftypn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpv9fmgaos/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv9fmgaos/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpw7mrb1rj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw7mrb1rj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpke9okwmi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpke9okwmi/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp83_8sz55/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp83_8sz55/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmph062q75p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph062q75p/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqi2quws2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqi2quws2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8xo42j9l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8xo42j9l/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnsi7xneu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnsi7xneu/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpn4ed4ioz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn4ed4ioz/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmps8nualau/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps8nualau/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkr8fhdjj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkr8fhdjj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmplvsp4azu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplvsp4azu/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcpluwbao/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcpluwbao/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp42uprkvp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp42uprkvp/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp34metjt1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp34metjt1/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfnbnlo9t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfnbnlo9t/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpumpp2e5x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpumpp2e5x/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6mr323jn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6mr323jn/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpufl83af_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpufl83af_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsxgkeao5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsxgkeao5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpayrpi5bc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpayrpi5bc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqqzngs0v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqqzngs0v/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpufdgsgf6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpufdgsgf6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcowt49lj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcowt49lj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpndj40fsm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpndj40fsm/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpy5sop19o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy5sop19o/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5vaxufac/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5vaxufac/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpx9q831z2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx9q831z2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxz4jqtie/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxz4jqtie/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3h_pqhta/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3h_pqhta/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpq46khsux/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq46khsux/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpk3s0r8iq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk3s0r8iq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbki2ducm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbki2ducm/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpc81h9mh5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc81h9mh5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmplxxrmjga/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplxxrmjga/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxr6620o3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxr6620o3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1t9nijlr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1t9nijlr/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwmrghdw5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwmrghdw5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdl8olusg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdl8olusg/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdz6fyz_z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdz6fyz_z/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpin_wcem9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpin_wcem9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkud7y_kd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkud7y_kd/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp508jt340/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp508jt340/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuvoiso_i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuvoiso_i/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpddcu3zqm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpddcu3zqm/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp13dqi19r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp13dqi19r/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqq8b32i9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqq8b32i9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpt5o6r2f4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt5o6r2f4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgh5r2u7d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgh5r2u7d/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpv2wrbk5k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv2wrbk5k/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2kvibcs3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2kvibcs3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6sbqpg_e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6sbqpg_e/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8h7fy7qf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8h7fy7qf/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcmkd3kxz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcmkd3kxz/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp627ja44e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp627ja44e/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmk7735ux/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmk7735ux/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpj3ntks1d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj3ntks1d/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpft22c9yn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpft22c9yn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6fbvfwb8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6fbvfwb8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmppvijaw_o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppvijaw_o/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnmvfpjok/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnmvfpjok/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpp57vcn0g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp57vcn0g/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpn2i0ycy8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn2i0ycy8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2p00ybpn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2p00ybpn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxuosuda2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxuosuda2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqi0saz1f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqi0saz1f/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9hv8qlmq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9hv8qlmq/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp21ghqpml/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp21ghqpml/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbt500q6o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbt500q6o/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4fhzgch_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4fhzgch_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkyz25lqr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkyz25lqr/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_jhz8q8v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_jhz8q8v/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpb5i6ox_i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb5i6ox_i/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdtbsx3q2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdtbsx3q2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3eb3q5rn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3eb3q5rn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmppb4og3gf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppb4og3gf/f2.bed) ----------------------------- Captured stderr call ----------------------------- Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. ____________ test_three_in_a_row[strandedness_chain8-method_chain8] ____________ [gw7] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', False) method_chain = ('set_intersect', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('set_intersect', 'set_intersect'), E gr=Empty PyRanges, # or any other generated value E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:140 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E (and 109 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BAAEYGTAAAADQAAg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ___________ test_three_in_a_row[strandedness_chain33-method_chain33] ___________ [gw8] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', False), method_chain = ('intersect', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('intersect', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:15 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:145 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:369 E (and 23 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAEECwEAAFEAAw==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ____________ test_three_in_a_row[strandedness_chain1-method_chain1] ____________ [gw5] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', False) method_chain = ('set_union', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('set_union', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/init.py:174 E (and 189 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2A0MlMsD5LlYWBgZMAEACdCAX4=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ___________ test_three_in_a_row[strandedness_chain21-method_chain21] ___________ [gw6] linux -- Python 3.12.6 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 880, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1722, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', False), | method_chain=('nearest', 'set_union'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 65537 | 65538 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=Empty PyRanges, | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | (and 182 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY5Qpc/dnYGAEQgYQBWbBeYyMEEFkzAgAOaUBOQ==') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3784, in set_union | gr = gr.merge(strand=strand) | ^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 360, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', False), | method_chain=('nearest', 'set_union'), | gr=Empty PyRanges, | gr2=Empty PyRanges, # or any other generated value | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:33 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | (and 284 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BAAEYUCgwAAD4AAw==') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________________ test_k_nearest[upstream-True-same-last] ____________________ [gw4] linux -- Python 3.12.6 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 880, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 510, in test_k_nearest | @pytest.mark.explore | ^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1722, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 548, in test_k_nearest | result = gr.k_nearest( | ^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2450, in k_nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 180, in _nearest | df = __nearest(d1, d2, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 115, in nearest_previous | lidx, ridx, dist = nearest_previous_idx(d1, d2, d1.__k__.values, ties) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 28, in nearest_previous_idx | lidx, ridx_pos, dist = k_nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/k_nearest.pyx", line 28, in sorted_nearest.src.k_nearest.k_nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_k_nearest( | nearest_how='upstream', | overlap=True, | strandedness='same', | ties='last', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:14 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:15 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:160 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:171 | (and 40 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2TABIxYxAAAZAAD') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 548, in test_k_nearest | result = gr.k_nearest( | ^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2450, in k_nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 180, in _nearest | df = __nearest(d1, d2, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 140, in nearest_next | lidx, ridx, dist = nearest_next_idx(d1, d2, d1.__k__.values, ties) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 56, in nearest_next_idx | lidx, ridx_pos, dist = k_nearest_next_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/k_nearest.pyx", line 55, in sorted_nearest.src.k_nearest.k_nearest_next_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_k_nearest( | nearest_how='upstream', | overlap=True, | strandedness='same', | ties='last', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:160 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:171 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:41 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:42 | (and 41 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2QAA0YGOGBkxBQCAACfAAc=') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpv0s7y7ok/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv0s7y7ok/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxwvzma30/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxwvzma30/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpl8f2as3r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl8f2as3r/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7bczwx8x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7bczwx8x/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpaisizhc0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaisizhc0/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7coav738/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7coav738/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuwq_t052/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuwq_t052/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpncoeuq5u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpncoeuq5u/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdhzauirw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdhzauirw/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7grsjxdt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7grsjxdt/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpx8lurqct/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx8lurqct/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2c_weeiv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2c_weeiv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmplpmslq2f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplpmslq2f/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfuxefqbd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfuxefqbd/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpefriku0e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpefriku0e/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5rsgr86l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5rsgr86l/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbb7ig9fw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbb7ig9fw/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmptimbueae/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptimbueae/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_udd0f6b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_udd0f6b/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_tizolyp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_tizolyp/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpg7vg7cur/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg7vg7cur/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpghcct4i_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpghcct4i_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvd5qewgv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvd5qewgv/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfgw6xat2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfgw6xat2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3hkqs3kd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3hkqs3kd/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxhbc3q62/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxhbc3q62/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmt4677yc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmt4677yc/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpg6h4or_j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg6h4or_j/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_i3t0hag/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_i3t0hag/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdqt1w5r0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdqt1w5r0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkj3yi_fh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkj3yi_fh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmppgt0dzge/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppgt0dzge/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmppyy0hf14/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppyy0hf14/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpo1snp_7x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo1snp_7x/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpy15d0y4h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy15d0y4h/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfe7uw2g_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfe7uw2g_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmysi9qwx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmysi9qwx/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpodnu6onw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpodnu6onw/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1g6x9are/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1g6x9are/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwna9h7uy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwna9h7uy/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp266o80a4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp266o80a4/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpi_7jnkzz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi_7jnkzz/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp43ri8m8j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp43ri8m8j/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwhbeq9ui/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwhbeq9ui/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmponzsdqh_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmponzsdqh_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmplo71y3g5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplo71y3g5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcf36a63u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcf36a63u/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpv29zhvai/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv29zhvai/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpb7__j96q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb7__j96q/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp61gismgu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp61gismgu/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2542ej5v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2542ej5v/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbclrissj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbclrissj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfs0vle_j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfs0vle_j/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp11y7bnfm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp11y7bnfm/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqxk31oo3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqxk31oo3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpr0ut1k5_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr0ut1k5_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgvt1p7mk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgvt1p7mk/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwwjt0yng/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwwjt0yng/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpt1jzyq7a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt1jzyq7a/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_nerfgou/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_nerfgou/f2.bed) ----------------------------- Captured stderr call ----------------------------- Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. ___________ test_three_in_a_row[strandedness_chain45-method_chain45] ___________ [gw10] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', False), method_chain = ('join', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:68: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2, suffix="_c") pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:292: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('join', 'nearest'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E | chr1 | 1 | 2 | a | 0 | + | E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 7 | 8 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:53 E (and 29 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2QAAkYG9l2TGcsZF2sCmYyMIAEYYEQjAkAMCIQLIqmES7BBBAHu2QMC') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 7884498 | 7888538 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') Empty PyRanges ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4 | 7 | a | 0 | ... | | chr1 | 4 | 7 | a | 0 | ... | | chr1 | 18 | 21 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 6 | 11 | a | 0 | ... | | chr1 | 6 | 10 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 6 | 11 | a | 0 | ... | | chr1 | 6 | 10 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 6 | a | 0 | ... | | chr1 | 1 | 6 | a | 0 | ... | | chr1 | 1 | 6 | a | 0 | ... | | chr1 | 1 | 6 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 1 | 7 | a | 0 | ... | | chr1 | 1 | 7 | a | 0 | ... | | chr1 | 1 | 7 | a | 0 | ... | | chr1 | 1 | 7 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 28 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 6 | a | 0 | ... | | chr1 | 1 | 6 | a | 0 | ... | | chr1 | 1 | 6 | a | 0 | ... | | chr1 | 1 | 6 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 1 | 7 | a | 0 | ... | | chr1 | 1 | 7 | a | 0 | ... | | chr1 | 1 | 7 | a | 0 | ... | | chr1 | 1 | 7 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 28 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') Empty PyRanges ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 6 | a | 0 | ... | | chr1 | 1 | 6 | a | 0 | ... | | chr1 | 1 | 6 | a | 0 | ... | | chr1 | 1 | 6 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 1 | 7 | a | 0 | ... | | chr1 | 1 | 7 | a | 0 | ... | | chr1 | 1 | 7 | a | 0 | ... | | chr1 | 1 | 7 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 28 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 6 | a | 0 | ... | | chr1 | 1 | 6 | a | 0 | ... | | chr1 | 1 | 6 | a | 0 | ... | | chr1 | 1 | 6 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 1 | 7 | a | 0 | ... | | chr1 | 1 | 7 | a | 0 | ... | | chr1 | 1 | 7 | a | 0 | ... | | chr1 | 1 | 7 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 28 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 6 | a | 0 | ... | | chr1 | 1 | 6 | a | 0 | ... | | chr1 | 1 | 6 | a | 0 | ... | | chr1 | 1 | 6 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 1 | 7 | a | 0 | ... | | chr1 | 1 | 7 | a | 0 | ... | | chr1 | 1 | 7 | a | 0 | ... | | chr1 | 1 | 7 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 28 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 7 | a | 0 | ... | | chr1 | 1 | 7 | a | 0 | ... | | chr1 | 1 | 7 | a | 0 | ... | | chr1 | 1 | 7 | a | 0 | ... | | chr1 | 1 | 7 | a | 0 | ... | | chr1 | 1 | 7 | a | 0 | ... | | chr1 | 1 | 7 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 7 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 7 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 7 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 7 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 7 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') Empty PyRanges ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 7 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 7 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 7 | a | 0 | ... | | chr1 | 1 | 7 | a | 0 | ... | | chr1 | 1 | 7 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') Empty PyRanges ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 7 | a | 0 | ... | | chr1 | 1 | 7 | a | 0 | ... | | chr1 | 1 | 7 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 7 | a | 0 | ... | | chr1 | 1 | 7 | a | 0 | ... | | chr1 | 1 | 7 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 7 | a | 0 | ... | | chr1 | 1 | 7 | a | 0 | ... | | chr1 | 1 | 7 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 7 | a | 0 | ... | | chr1 | 1 | 7 | a | 0 | ... | | chr1 | 1 | 7 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 7 | a | 0 | ... | | chr1 | 1 | 7 | a | 0 | ... | | chr1 | 1 | 7 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 7 | a | 0 | ... | | chr1 | 1 | 7 | a | 0 | ... | | chr1 | 1 | 7 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 258 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 7 | a | 0 | ... | | chr1 | 1 | 7 | a | 0 | ... | | chr1 | 1 | 7 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 7 | a | 0 | ... | | chr1 | 1 | 7 | a | 0 | ... | | chr1 | 1 | 7 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 7 | a | 0 | ... | | chr1 | 1 | 7 | a | 0 | ... | | chr1 | 1 | 7 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 7 | a | 0 | ... | | chr1 | 1 | 7 | a | 0 | ... | | chr1 | 1 | 7 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________________________ test_set_intersect[same] ___________________________ [gw0] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness = 'same' @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness", no_opposite) tests/test_binary.py:113: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:128: in test_set_intersect result = gr.set_intersect(gr2, strandedness=strandedness) pyranges/pyranges.py:3687: in set_intersect self_clusters = self.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_set_intersect( E # The test always failed when commented parts were varied together. E strandedness='same', E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., # or any other generated value E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., # or any other generated value E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2TABIxYxAAAZAAD') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpee7qtm1u/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpee7qtm1u/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpmoi904lh/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpmoi904lh/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpbyovr3p_/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpbyovr3p_/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmptlq9csco/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmptlq9csco/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpwg8krsnx/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpwg8krsnx/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpnyis3zpx/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpnyis3zpx/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp5o5hkoki/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp5o5hkoki/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp1tf9hqpt/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp1tf9hqpt/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpoiwsis2q/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpoiwsis2q/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpt0zwhq8u/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpt0zwhq8u/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp61vz0bdi/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp61vz0bdi/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpiairr3ul/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpiairr3ul/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpdrju7we7/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpdrju7we7/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp4mawj3wf/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp4mawj3wf/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp8hpy8b3m/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp8hpy8b3m/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmptr1q2m0p/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmptr1q2m0p/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpd_365m7h/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpd_365m7h/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmplozm8pw9/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmplozm8pw9/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp_987rr11/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp_987rr11/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmphpl4ykdv/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmphpl4ykdv/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmprdlk5iwt/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmprdlk5iwt/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpivinpcy2/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpivinpcy2/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpac4hsr12/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpac4hsr12/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpklubmjoa/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpklubmjoa/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpsgd0n7ck/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpsgd0n7ck/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp44uiq2f8/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp44uiq2f8/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp3ro2m731/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp3ro2m731/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpbv6r702p/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpbv6r702p/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpsm97rl07/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpsm97rl07/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmphf1vlk8m/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmphf1vlk8m/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpgjutky3w/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpgjutky3w/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpvou3aj_e/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpvou3aj_e/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp1h9j4tm7/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp1h9j4tm7/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpfr1tzb_v/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpfr1tzb_v/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpkc68kcp3/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpkc68kcp3/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpy5mxiufh/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpy5mxiufh/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpyzg42ow1/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpyzg42ow1/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp7wn6k8u4/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp7wn6k8u4/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp8moc125n/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp8moc125n/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp04z3jind/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp04z3jind/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpcxtfl6el/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpcxtfl6el/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpy_0kyfb8/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpy_0kyfb8/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpxlxorezz/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpxlxorezz/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpogot27o9/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpogot27o9/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpaxyhqos6/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpaxyhqos6/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp09976k4x/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp09976k4x/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpmzl2_qdc/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpmzl2_qdc/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpqs_x3ziu/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpqs_x3ziu/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpeklhu6zm/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpeklhu6zm/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp2w78ts5y/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp2w78ts5y/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpcvr08q_t/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpcvr08q_t/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmph7pq30d7/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmph7pq30d7/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp4ojpha47/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp4ojpha47/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpfv99wd3d/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpfv99wd3d/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpbuh_02xp/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpbuh_02xp/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmphvpainau/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmphvpainau/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmptf9e_k0b/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmptf9e_k0b/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpnfdh9adm/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpnfdh9adm/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpgpnjv0k_/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpgpnjv0k_/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpyzhv4xgx/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpyzhv4xgx/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpem0n1s59/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpem0n1s59/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp7quf665m/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp7quf665m/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmptnitqm9x/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmptnitqm9x/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpuld9noil/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpuld9noil/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp6fadm706/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp6fadm706/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp6x21uag5/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp6x21uag5/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpsyx74cw0/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpsyx74cw0/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp63r3zemf/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp63r3zemf/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp_x38s_u9/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp_x38s_u9/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmps2ecrtg8/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmps2ecrtg8/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmppt9wy1fk/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmppt9wy1fk/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp1shui5m2/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp1shui5m2/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpazsfvt4c/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpazsfvt4c/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp934wmv0u/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp934wmv0u/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp8blwxijl/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp8blwxijl/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpwalpqkn_/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpwalpqkn_/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpdx9p6mys/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpdx9p6mys/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpul_94ujt/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpul_94ujt/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp0we4j4p0/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp0we4j4p0/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp0o1hz9vf/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp0o1hz9vf/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpjb13q9fh/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpjb13q9fh/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpxitio0xk/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpxitio0xk/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmphxvwkb3a/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmphxvwkb3a/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpmpo5cbkv/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpmpo5cbkv/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpjtwufrzh/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpjtwufrzh/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpeg_80pgm/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpeg_80pgm/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpgz6ig_3j/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpgz6ig_3j/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp1ech2i7z/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp1ech2i7z/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpege3uszi/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpege3uszi/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp3u60l1xv/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp3u60l1xv/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpus6nn7hw/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpus6nn7hw/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpwjt4_0yn/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpwjt4_0yn/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp151y68hx/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp151y68hx/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpwh9vinxe/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpwh9vinxe/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpve1441jh/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpve1441jh/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpr3qc8qlv/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpr3qc8qlv/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp53yzmls_/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp53yzmls_/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpx4v80qir/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpx4v80qir/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpc25hjldx/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpc25hjldx/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpsbuxmrr6/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpsbuxmrr6/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp5605d7d5/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp5605d7d5/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmppjwl4cn2/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmppjwl4cn2/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp8k20w97v/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp8k20w97v/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpp_poocko/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpp_poocko/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp0_iugcow/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp0_iugcow/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpmq_pfb4y/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpmq_pfb4y/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp1gl4id2x/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp1gl4id2x/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp59w398cf/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp59w398cf/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpwdlvqdpb/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpwdlvqdpb/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpk7z2_363/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpk7z2_363/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp94gb61am/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp94gb61am/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpfq2krd5n/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpfq2krd5n/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpale8g0_d/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpale8g0_d/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpxj5x3w6i/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpxj5x3w6i/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmprvvrrsat/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmprvvrrsat/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpp9a6_nvr/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpp9a6_nvr/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpvlmdve7x/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpvlmdve7x/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp02u57ji1/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp02u57ji1/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp6x4c_hi6/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp6x4c_hi6/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpqxn1zb7o/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpqxn1zb7o/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpl8xxjjeb/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpl8xxjjeb/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpify91jpt/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpify91jpt/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpi7bk2ah_/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpi7bk2ah_/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp45vyjxqf/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp45vyjxqf/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp91qb1uc8/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp91qb1uc8/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpgdxode6w/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpgdxode6w/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp2k3pk8_j/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp2k3pk8_j/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpfka_qbvr/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpfka_qbvr/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp8t5gp_bi/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp8t5gp_bi/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpv15jpoaj/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpv15jpoaj/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpzqqg2d78/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpzqqg2d78/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpqhxsuhhk/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpqhxsuhhk/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpbgantb65/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpbgantb65/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpzqxd8588/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpzqxd8588/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpvwrw5wxh/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpvwrw5wxh/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp0nf2g5xk/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp0nf2g5xk/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp1y4ja5f2/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp1y4ja5f2/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp3rlv5_o4/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp3rlv5_o4/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpnhw0uf3d/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpnhw0uf3d/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp6099v7xg/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp6099v7xg/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpmrsvawu_/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpmrsvawu_/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpxi65sz7e/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpxi65sz7e/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpnz9tr3o5/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpnz9tr3o5/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpg3x27sm5/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpg3x27sm5/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpzxdikpxv/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpzxdikpxv/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpni30549f/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpni30549f/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmptgflo9mp/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmptgflo9mp/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpq4nr7e25/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpq4nr7e25/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpbjk1vrgs/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpbjk1vrgs/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpdgflrno9/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpdgflrno9/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp_ioy_ek4/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp_ioy_ek4/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp3sb5dl3_/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp3sb5dl3_/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpcy9i4x_u/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpcy9i4x_u/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpi6srqisf/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpi6srqisf/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpvmwvb3qe/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpvmwvb3qe/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp3innic73/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp3innic73/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmph5kou6_d/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmph5kou6_d/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp2x270qyz/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp2x270qyz/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpd9vtifj8/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpd9vtifj8/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmphhyex36e/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmphhyex36e/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp2gv4a3d0/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp2gv4a3d0/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpssrorp_9/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpssrorp_9/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp_ihp9p_j/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp_ihp9p_j/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpsteq3z1a/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpsteq3z1a/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpf1p4kddc/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpf1p4kddc/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpxied5bjw/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpxied5bjw/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp4xp9vyui/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp4xp9vyui/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp8_9bi3w9/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp8_9bi3w9/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp0dom55df/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp0dom55df/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp96xpr7nc/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp96xpr7nc/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpi53inlw1/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpi53inlw1/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpbftqvpp7/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpbftqvpp7/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpqw13s8z0/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpqw13s8z0/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpn09bp__f/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpn09bp__f/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpnok_dl6w/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpnok_dl6w/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpyu_nkaar/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpyu_nkaar/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp41wx6jpy/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp41wx6jpy/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpniramihd/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpniramihd/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp0bvwyhps/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp0bvwyhps/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpgfnc1olo/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpgfnc1olo/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp5nt4baj9/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp5nt4baj9/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp2sdy9m29/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp2sdy9m29/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpuymny4kj/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpuymny4kj/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp69kgx6nl/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp69kgx6nl/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpsrecmszb/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpsrecmszb/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpsyabli31/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpsyabli31/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpjigx_gpu/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpjigx_gpu/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmplc5soz22/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmplc5soz22/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp_nk2kq6b/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp_nk2kq6b/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpztax25ef/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpztax25ef/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmplbryylkd/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmplbryylkd/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpmp58ruc2/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpmp58ruc2/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpl_2ag1gh/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpl_2ag1gh/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpyyw3d6on/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpyyw3d6on/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmprzshw5kh/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmprzshw5kh/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpjk8mxfzl/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpjk8mxfzl/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpe18xqroo/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpe18xqroo/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp26_mx369/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp26_mx369/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp3d0mj97i/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp3d0mj97i/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmphv3lpryh/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmphv3lpryh/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmplgcs9yn8/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmplgcs9yn8/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp_yfq4ohm/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp_yfq4ohm/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpu1uyr_0y/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpu1uyr_0y/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpu6ouajkj/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpu6ouajkj/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp0k8qo9vz/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp0k8qo9vz/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpq2unfwn8/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpq2unfwn8/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmphvahqy11/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmphvahqy11/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpuwl5sd6v/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpuwl5sd6v/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpsw4svntx/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpsw4svntx/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpwq8y194f/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpwq8y194f/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmps3eb8kiq/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmps3eb8kiq/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpsyjrsfar/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpsyjrsfar/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp9dmmlj__/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp9dmmlj__/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpizv90s32/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpizv90s32/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpaqr9esfw/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpaqr9esfw/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp161fr_h9/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp161fr_h9/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp6tmja9v7/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp6tmja9v7/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp9zkyttsx/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp9zkyttsx/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpqwifaga5/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpqwifaga5/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpf2j1qcg_/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpf2j1qcg_/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpb2_sez30/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpb2_sez30/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp4bpzvhow/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp4bpzvhow/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmplhb27vhd/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmplhb27vhd/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmph3i2y1bl/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmph3i2y1bl/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmplcn2n0n3/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmplcn2n0n3/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpfpz8p4_q/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpfpz8p4_q/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpvj98s85m/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpvj98s85m/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp60mojmds/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp60mojmds/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpvr9h8iz8/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpvr9h8iz8/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp6kp4v1hg/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp6kp4v1hg/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpp2xe_m91/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpp2xe_m91/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp84ondnoh/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp84ondnoh/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp1g3jpl4p/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp1g3jpl4p/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpc2r_h8pu/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpc2r_h8pu/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpjyl3fk8_/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpjyl3fk8_/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpchaq4mnf/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpchaq4mnf/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp9m4si0rv/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp9m4si0rv/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpouutkhmt/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpouutkhmt/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpjv40gawv/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpjv40gawv/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp362tfwn2/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp362tfwn2/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpop1fa7vf/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpop1fa7vf/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp5mlh1zrt/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp5mlh1zrt/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpnebqdpq_/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpnebqdpq_/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp23q2rf6r/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp23q2rf6r/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpig3m_tg6/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpig3m_tg6/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpp2lft142/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpp2lft142/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpgv27hvou/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpgv27hvou/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp57x3ze91/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp57x3ze91/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpto6zp14n/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpto6zp14n/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpp3kwk426/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpp3kwk426/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp_nuoziv_/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp_nuoziv_/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpz65kw3no/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpz65kw3no/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp644tgccu/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp644tgccu/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpths1p2sp/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpths1p2sp/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmprnkbc5fc/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmprnkbc5fc/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpr4gkl9_2/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpr4gkl9_2/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp2ec1g3de/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp2ec1g3de/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp36k8h4mv/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp36k8h4mv/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpo9miipub/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpo9miipub/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp2c47v9hf/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp2c47v9hf/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpyk_8skaj/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpyk_8skaj/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp3_du41gd/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp3_du41gd/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp2l7aob7t/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp2l7aob7t/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp67x7814q/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp67x7814q/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpfn_28roi/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpfn_28roi/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp29qqtha1/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp29qqtha1/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpx34ur0jl/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpx34ur0jl/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpcqmkcy97/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpcqmkcy97/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpd7mu89p3/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpd7mu89p3/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpc_zyo2qy/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpc_zyo2qy/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpqac02_c1/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpqac02_c1/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpfyu3r0xm/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpfyu3r0xm/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpah7nxm0k/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpah7nxm0k/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpshxea50y/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpshxea50y/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpdb1gpq6v/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpdb1gpq6v/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpqjmp4y45/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpqjmp4y45/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpkkzmz9as/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpkkzmz9as/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpg6l7plx2/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpg6l7plx2/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpe3wx9zjd/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpe3wx9zjd/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpfs9uc60y/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpfs9uc60y/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp8y6fer7q/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp8y6fer7q/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmppvta52fn/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmppvta52fn/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpm9e4ym2m/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpm9e4ym2m/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpyrb6pm9x/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpyrb6pm9x/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp_c5kor3j/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp_c5kor3j/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpms24rw42/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpms24rw42/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpdlkgohz0/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpdlkgohz0/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpsz3o9r9d/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpsz3o9r9d/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp3lqy0oos/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp3lqy0oos/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpg036efed/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpg036efed/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpve694e7t/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpve694e7t/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpa47emf19/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpa47emf19/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpwcpiwvlv/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpwcpiwvlv/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpncegzlr0/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpncegzlr0/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpuf2wyy6o/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpuf2wyy6o/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpwbybbcfo/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpwbybbcfo/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpq_1iyvn7/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpq_1iyvn7/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp62e3udlo/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp62e3udlo/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpznty3597/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpznty3597/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp35tgmvdd/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp35tgmvdd/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp271ejbgf/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp271ejbgf/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpkrqup_wb/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpkrqup_wb/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpi9oi4ynu/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpi9oi4ynu/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpe9ytrlct/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpe9ytrlct/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp22m6ui_2/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp22m6ui_2/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpzkp8g1tq/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpzkp8g1tq/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpbdpndgk7/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpbdpndgk7/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpldgxmyct/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpldgxmyct/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpzvpe9983/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpzvpe9983/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpxj4hoim4/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpxj4hoim4/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp9ntwm_yp/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp9ntwm_yp/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpulbejrsn/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpulbejrsn/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpwlbbdxt3/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpwlbbdxt3/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpr5nqs53z/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpr5nqs53z/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp78y9f4sp/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp78y9f4sp/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpm7itc2nm/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpm7itc2nm/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp09ej_nyh/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp09ej_nyh/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpadmi16tj/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpadmi16tj/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpvi467dc2/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpvi467dc2/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpd53qga5j/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpd53qga5j/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpe6rup19v/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpe6rup19v/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp6u5y933w/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp6u5y933w/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpkfjjr84o/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpkfjjr84o/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpf8ahluh8/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpf8ahluh8/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpaoqno1e5/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpaoqno1e5/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpbt_tbssr/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpbt_tbssr/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpvt_5uvof/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpvt_5uvof/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmphdcooc7m/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmphdcooc7m/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpty_fm513/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpty_fm513/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp1qlx4u43/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp1qlx4u43/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmppi9mjq5l/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmppi9mjq5l/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp1trg9x6t/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp1trg9x6t/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpmzw8i7kf/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpmzw8i7kf/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpan14yp47/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpan14yp47/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmprk45oycf/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmprk45oycf/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpkhaocsjy/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpkhaocsjy/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpakojaccv/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpakojaccv/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp0x4pcv6_/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp0x4pcv6_/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpxbcn3y6s/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpxbcn3y6s/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp1fy4fjer/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp1fy4fjer/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmplf7xq5yc/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmplf7xq5yc/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpxmo0uz7h/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpxmo0uz7h/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp87x9im1h/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp87x9im1h/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp1mkj9jq7/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp1mkj9jq7/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpfwk6a52x/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpfwk6a52x/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpvlpqo6sj/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpvlpqo6sj/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmplp8n6z8w/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmplp8n6z8w/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpzw6ck2ni/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpzw6ck2ni/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpcd8yb5jn/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpcd8yb5jn/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp4v2e9o1r/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp4v2e9o1r/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpnud4zkgz/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpnud4zkgz/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmppq6g0od5/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmppq6g0od5/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpi5ibugis/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpi5ibugis/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpi_ff1qp7/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpi_ff1qp7/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpd33g9rxc/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpd33g9rxc/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp908g4ilc/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp908g4ilc/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpv804zuiq/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpv804zuiq/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp2wkrfzxc/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp2wkrfzxc/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp6mocn1tp/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp6mocn1tp/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpy4k1cwec/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpy4k1cwec/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp9ocha5c5/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp9ocha5c5/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpe0vjf1y9/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpe0vjf1y9/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpgs5ftq0d/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpgs5ftq0d/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpnw9jr80y/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpnw9jr80y/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp6n9upg79/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp6n9upg79/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpkk0486k_/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpkk0486k_/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmphqrnq1hb/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmphqrnq1hb/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpg6c2ly8u/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpg6c2ly8u/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp7qc8v_ui/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp7qc8v_ui/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpztqpcer3/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpztqpcer3/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp6s0st368/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp6s0st368/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp34q1g4yv/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp34q1g4yv/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp91vnsu8n/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp91vnsu8n/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp2yfn8vz9/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp2yfn8vz9/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpu4r_u1d7/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpu4r_u1d7/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpt6woim_t/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpt6woim_t/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpurk1_4uk/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpurk1_4uk/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmppbkcwytw/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmppbkcwytw/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpxmemc6fd/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpxmemc6fd/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpj11y_rlv/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpj11y_rlv/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpidcssioc/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpidcssioc/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpmu776jxc/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpmu776jxc/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpewwi8hjr/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpewwi8hjr/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp8thnsbop/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp8thnsbop/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpkj2icfqm/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpkj2icfqm/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp5j23l1uh/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp5j23l1uh/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpg9tg_gfn/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpg9tg_gfn/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpqafvtl82/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpqafvtl82/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp3o3pb2el/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp3o3pb2el/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp07bnhqfi/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp07bnhqfi/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp5vzxah5j/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp5vzxah5j/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp37rnohok/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp37rnohok/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp5z63ulum/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp5z63ulum/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpcisn0o5o/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpcisn0o5o/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpp4i8y6l9/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpp4i8y6l9/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp7gv2jdre/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp7gv2jdre/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpfj_bgd9h/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpfj_bgd9h/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp0q_r2cde/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp0q_r2cde/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpzisnwlj6/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpzisnwlj6/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp7ygps8lt/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp7ygps8lt/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpejyf2o9g/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpejyf2o9g/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmph_1fhp49/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmph_1fhp49/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpu88ep8dd/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpu88ep8dd/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpgl92pmao/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpgl92pmao/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp2nlc73j_/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp2nlc73j_/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmprzzs1qhd/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmprzzs1qhd/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpx5djhquv/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpx5djhquv/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpvf3t7c89/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpvf3t7c89/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpuxjh5blv/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpuxjh5blv/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpejsn43ly/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpejsn43ly/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp2_iurkfs/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp2_iurkfs/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpx4jx7rrv/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpx4jx7rrv/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpgp9xc_5a/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpgp9xc_5a/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp5_c9wa_2/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp5_c9wa_2/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp12it7jzp/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp12it7jzp/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpf_680a4v/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpf_680a4v/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp5z34idc6/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp5z34idc6/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp3nq_8mmz/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp3nq_8mmz/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) ___________ test_three_in_a_row[strandedness_chain57-method_chain57] ___________ [gw9] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', 'same') method_chain = ('set_intersect', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('set_intersect', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E /usr/lib/python3/dist-packages/natsort/utils.py:344 E (and 103 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2Dki0mT0JLKYmBgZMAEACk5AZk=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') _____________________ test_nearest[upstream-True-opposite] _____________________ [gw2] linux -- Python 3.12.6 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 880, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 323, in test_nearest | @pytest.mark.parametrize("nearest_how,overlap,strandedness", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1722, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 3 distinct failures. (3 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 351, in test_nearest | result = gr.nearest( | ^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 118, in _nearest | r_idx, dist = _previous_nonoverlapping(df_to_find_nearest_in.Start, | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_nearest( | nearest_how='upstream', | overlap=True, | strandedness='opposite', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | (and 126 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2QAA0Y4gU6BmQAApQAH') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 351, in test_nearest | result = gr.nearest( | ^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 115, in _nearest | r_idx, dist = _next_nonoverlapping(df_to_find_nearest_in.End, | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 62, in _next_nonoverlapping | r_idx, dist = nearest_next_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 34, in sorted_nearest.src.sorted_nearest.nearest_next_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_nearest( | nearest_how='upstream', | overlap=True, | strandedness='opposite', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | (and 127 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2QAA0YGOGBkRBKCsgEApQAH') as a decorator on your test case +---------------- 3 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 359, in test_nearest | compare_results_nearest(bedtools_df, result) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 107, in compare_results_nearest | assert_df_equal(result_df, bedtools_df) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/helpers.py", line 60, in assert_df_equal | pd.testing.assert_frame_equal(df1, df2) | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 1279, in assert_frame_equal | assert_series_equal( | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 975, in assert_series_equal | assert_attr_equal("dtype", left, right, obj=f"Attributes of {obj}") | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 421, in assert_attr_equal | raise_assert_detail(obj, msg, left_attr, right_attr) | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 614, in raise_assert_detail | raise AssertionError(msg) | AssertionError: Attributes of DataFrame.iloc[:, 4] (column name="Distance") are different | | Attribute "dtype" are different | [left]: int32 | [right]: int64 | Falsifying example: test_nearest( | nearest_how='upstream', | overlap=True, | strandedness='opposite', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | (and 459 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2QAA0YGBGDEEGIEAACLAAY=') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpti1quubh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpti1quubh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp36j25hm3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp36j25hm3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpt78i4o11/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt78i4o11/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0_dmweak/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0_dmweak/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfqjlkh47/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfqjlkh47/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbwavt9m5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbwavt9m5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5gkdltyb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5gkdltyb/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgyxayibh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgyxayibh/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmps26bhhfb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps26bhhfb/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpx6l1lwon/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx6l1lwon/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdzsbx68i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdzsbx68i/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpl069tvk3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl069tvk3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjowf66ho/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjowf66ho/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxw5tgio5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxw5tgio5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphxwjj43f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphxwjj43f/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7ypdyzx6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7ypdyzx6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpc75s3zjj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc75s3zjj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1do20onh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1do20onh/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpflogmymb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpflogmymb/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9g_8ylyy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9g_8ylyy/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfl1q3yth/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfl1q3yth/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpiix7dpnx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiix7dpnx/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgs08nped/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgs08nped/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppn16u7e6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppn16u7e6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpx_soq8y_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx_soq8y_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6i6hgyjh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6i6hgyjh/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmu54l6_h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmu54l6_h/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpl2ukuamq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl2ukuamq/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptrxikae7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptrxikae7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpei26gktt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpei26gktt/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpk_werx5n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk_werx5n/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpg2ohus4h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg2ohus4h/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpf4ubvi9m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf4ubvi9m/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6kmfdfbp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6kmfdfbp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvlfttwft/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvlfttwft/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmps8gmww2t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps8gmww2t/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnlpzg6q1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnlpzg6q1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0gohk33x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0gohk33x/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpertvtj_r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpertvtj_r/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyuwvyzq0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyuwvyzq0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjdyo3k55/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjdyo3k55/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppuzyg1ry/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppuzyg1ry/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptoisar03/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptoisar03/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1az77aw_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1az77aw_/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjop55j29/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjop55j29/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2jaajtua/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2jaajtua/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0lmjcniq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0lmjcniq/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_vodg6ue/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_vodg6ue/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9h38idgd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9h38idgd/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7oi9n1xd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7oi9n1xd/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1ym7_iap/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1ym7_iap/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphuiy3cdp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphuiy3cdp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_kjva1cd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_kjva1cd/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3n18go5s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3n18go5s/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjw63fx33/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjw63fx33/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpk_fozait/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk_fozait/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjbr1pk60/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjbr1pk60/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprp25_ws1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprp25_ws1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprvejm72i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprvejm72i/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpki_mhw6e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpki_mhw6e/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyub0cud0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyub0cud0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmzvhvxq_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmzvhvxq_/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpasi_03i3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpasi_03i3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0ovhghc0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0ovhghc0/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpk3oh5iio/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk3oh5iio/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0mrbfyku/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0mrbfyku/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpffzudepe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpffzudepe/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptxi9lyde/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptxi9lyde/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpj3gnpc9s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj3gnpc9s/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp86bzmc9x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp86bzmc9x/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqzv0vt87/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqzv0vt87/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe_uzt9kj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe_uzt9kj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbov0tliq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbov0tliq/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpf_wt6hau/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf_wt6hau/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvjkwyhqq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvjkwyhqq/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdgcavqdb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdgcavqdb/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpg6l4qnd0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg6l4qnd0/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpclvsbmmk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpclvsbmmk/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnewduu46/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnewduu46/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpm6b4lp1_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm6b4lp1_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpspydpjn0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpspydpjn0/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdhnyxj3r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdhnyxj3r/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphz9c25ss/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphz9c25ss/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfqnjhq8b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfqnjhq8b/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphye8dypf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphye8dypf/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpaw8fcjcv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaw8fcjcv/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3eihh5ji/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3eihh5ji/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp107yzewr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp107yzewr/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpp5ueugmx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp5ueugmx/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbr3npgzb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbr3npgzb/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsw84yw4_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsw84yw4_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpelj40wtq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpelj40wtq/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbpmlu7ph/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbpmlu7ph/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpg1cp9dpp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg1cp9dpp/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpznu9souq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpznu9souq/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5kbzn2pc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5kbzn2pc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpse2bkhhf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpse2bkhhf/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzr3i7bfz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzr3i7bfz/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4tgbnhgw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4tgbnhgw/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_uit5etw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_uit5etw/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuy038mnu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuy038mnu/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr2 1 258 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr2 | 1 | 258 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr2 1 258 - 0 df2 Chromosome Start End Strand Distance 0 chr2 1 258 - 0 Actual Chromosome Start End Strand Distance 0 chr2 1 258 - 0 Expected Chromosome Start End Strand Distance 0 chr2 1 258 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6ts81_qy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6ts81_qy/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_i7n0as9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_i7n0as9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpntzvhswu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpntzvhswu/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0dk5f4mg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0dk5f4mg/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyfxm71su/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyfxm71su/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4ojowcik/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4ojowcik/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcap_86va/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcap_86va/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4yklcorb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4yklcorb/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpa3tn2bj_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa3tn2bj_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2q7d0ccn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2q7d0ccn/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpaweombj4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaweombj4/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr2 1 258 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr2 | 1 | 258 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr2 1 258 - 0 df2 Chromosome Start End Strand Distance 0 chr2 1 258 - 0 Actual Chromosome Start End Strand Distance 0 chr2 1 258 - 0 Expected Chromosome Start End Strand Distance 0 chr2 1 258 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpengxqctn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpengxqctn/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxwxbw83z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxwxbw83z/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjdk6sld7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjdk6sld7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpc8jkzxor/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc8jkzxor/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpi60xtf66/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi60xtf66/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbszn2tvy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbszn2tvy/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr2 1 258 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr2 | 1 | 258 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr2 1 258 - 0 df2 Chromosome Start End Strand Distance 0 chr2 1 258 - 0 Actual Chromosome Start End Strand Distance 0 chr2 1 258 - 0 Expected Chromosome Start End Strand Distance 0 chr2 1 258 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1obrhwjo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1obrhwjo/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr2 1 258 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr2 | 1 | 258 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr2 1 258 - 0 df2 Chromosome Start End Strand Distance 0 chr2 1 258 - 0 Actual Chromosome Start End Strand Distance 0 chr2 1 258 - 0 Expected Chromosome Start End Strand Distance 0 chr2 1 258 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1xvcblom/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1xvcblom/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr2 1 258 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr2 | 1 | 258 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr2 1 258 - 0 df2 Chromosome Start End Strand Distance 0 chr2 1 258 - 0 Actual Chromosome Start End Strand Distance 0 chr2 1 258 - 0 Expected Chromosome Start End Strand Distance 0 chr2 1 258 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4_fbe2bb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4_fbe2bb/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr2 1 258 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr2 | 1 | 258 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr2 1 258 - 0 df2 Chromosome Start End Strand Distance 0 chr2 1 258 - 0 Actual Chromosome Start End Strand Distance 0 chr2 1 258 - 0 Expected Chromosome Start End Strand Distance 0 chr2 1 258 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1wz9oz3e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1wz9oz3e/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8v4cdlo2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8v4cdlo2/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr2 1 258 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr2 | 1 | 258 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr2 1 258 - 0 df2 Chromosome Start End Strand Distance 0 chr2 1 258 - 0 Actual Chromosome Start End Strand Distance 0 chr2 1 258 - 0 Expected Chromosome Start End Strand Distance 0 chr2 1 258 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjhifcptf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjhifcptf/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpm999f32i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm999f32i/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr2 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr2 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr2 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr2 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr2 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr2 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpml1f28nb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpml1f28nb/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr2 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr2 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr2 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr2 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr2 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr2 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqrdx85k7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqrdx85k7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp39707vrq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp39707vrq/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpw5fo0863/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw5fo0863/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpr7iiqi_4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr7iiqi_4/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfdese4qn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfdese4qn/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpeujo3qji/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpeujo3qji/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpa2r16jya/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa2r16jya/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmsimd78s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmsimd78s/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpr6xqae9d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr6xqae9d/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr2 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr2 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr2 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr2 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr2 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr2 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprjtf0hgr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprjtf0hgr/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1_ncwfvq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1_ncwfvq/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpx3gqiegl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx3gqiegl/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr2 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr2 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr2 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr2 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr2 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr2 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdhucaldc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdhucaldc/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr2 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr2 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr2 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr2 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr2 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr2 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuztti3fw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuztti3fw/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr2 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr2 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr2 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr2 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr2 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr2 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpitwgp_xi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpitwgp_xi/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr2 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr2 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr2 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr2 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr2 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr2 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptpqu2vkd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptpqu2vkd/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpem_3crrw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpem_3crrw/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpggqifjsu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpggqifjsu/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_7w9dl2q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_7w9dl2q/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpetlr4lkk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpetlr4lkk/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkd01pcaj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkd01pcaj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxtri810x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxtri810x/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4dglkuhj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4dglkuhj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjlfk2u6w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjlfk2u6w/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgokjnkg0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgokjnkg0/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfp8lab5f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfp8lab5f/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppahqs_10/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppahqs_10/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpt0k9ejfm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt0k9ejfm/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpu4imbin7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu4imbin7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpei_el0tp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpei_el0tp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5m67iyfm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5m67iyfm/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbpuu9oe8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbpuu9oe8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpn1e82qwm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn1e82qwm/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 3 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 3 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 3 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 3 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 3 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwznybc59/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwznybc59/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpow_b4c04/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpow_b4c04/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplf264zic/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplf264zic/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcgm7_sg_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcgm7_sg_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpi9ucnbrp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi9ucnbrp/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmbo5cy9r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmbo5cy9r/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmph5a2qrtm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph5a2qrtm/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 3 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 3 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 3 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 3 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 3 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppr017dpg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppr017dpg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwenreyig/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwenreyig/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpp5o4bhtr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp5o4bhtr/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpicxh6gcp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpicxh6gcp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpq964pv46/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq964pv46/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuii74dz2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuii74dz2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6emjrqzo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6emjrqzo/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdh7pxx3n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdh7pxx3n/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ____________ test_three_in_a_row[strandedness_chain9-method_chain9] ____________ [gw7] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', False) method_chain = ('set_intersect', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('set_intersect', 'overlap'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E (and 65 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2D09xc0N2K5yMDIgAUAADFTAfA=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ___________________________ test_coverage[opposite] ____________________________ [gw1] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness = 'opposite' @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness", strandedness) tests/test_binary.py:207: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:238: in test_coverage result = gr.coverage(gr2, strandedness=strandedness) pyranges/pyranges.py:1341: in coverage other = other.merge(count=True, strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_coverage( E strandedness='opposite', E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., # or any other generated value E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., # or any other generated value E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2TABIxYxAAAZAAD') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpwjf97uax/f1.bed -b /tmp/tmpwjf97uax/f2.bed Chromosome Start End Name Score Strand 0 chr1 2454285 2459049 a 0 - 1 chr1 8519971 8520354 a 0 - 2 chr4 870895 880391 a 0 + 3 chr4 9859978 9869474 a 0 - 4 chr10 9201199 9204016 a 0 + 5 chr12 6580064 6589560 a 0 + 6 chr20 9038869 9041803 a 0 - 7 chr21 337599 346807 a 0 + 8 chr22 5878009 5884211 a 0 + Chromosome Start End Name Score Strand 0 chr1 1208662 1218013 a 0 + 1 chr1 1084855 1091258 a 0 - 2 chr7 2630459 2630862 a 0 + 3 chr11 7296742 7304508 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp4kw0hvtl/f1.bed -b /tmp/tmp4kw0hvtl/f2.bed Chromosome Start End Name Score Strand 0 chr1 2454285 2459049 a 0 - 1 chr4 870895 880391 a 0 + 2 chr4 8519971 8520354 a 0 - 3 chr4 9859978 9869474 a 0 - 4 chr10 9201199 9204016 a 0 + 5 chr12 6580064 6589560 a 0 + 6 chr20 9038869 9041803 a 0 - 7 chr21 337599 346807 a 0 + 8 chr22 5878009 5884211 a 0 + Chromosome Start End Name Score Strand 0 chr1 1208662 1218013 a 0 + 1 chr1 1084855 1091258 a 0 - 2 chr7 2630459 2630862 a 0 + 3 chr11 7296742 7304508 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpyxqrr8s_/f1.bed -b /tmp/tmpyxqrr8s_/f2.bed Chromosome Start End Name Score Strand 0 chr1 2454285 2459049 a 0 - 1 chr4 870895 880391 a 0 + 2 chr4 8519971 8520354 a 0 - 3 chr4 9859978 9869474 a 0 - 4 chr10 9201199 9204016 a 0 + 5 chr12 6580064 6589560 a 0 + 6 chr20 9038869 9041803 a 0 - 7 chr21 337599 346807 a 0 + 8 chr22 5878009 5884211 a 0 + Chromosome Start End Name Score Strand 0 chr1 2454285 2459049 a 0 - 1 chr4 870895 880391 a 0 + 2 chr4 8519971 8520354 a 0 - 3 chr4 9859978 9869474 a 0 - 4 chr10 9201199 9204016 a 0 + 5 chr12 6580064 6589560 a 0 + 6 chr20 9038869 9041803 a 0 - 7 chr21 337599 346807 a 0 + 8 chr22 5878009 5884211 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpdx5wvf7m/f1.bed -b /tmp/tmpdx5wvf7m/f2.bed Chromosome Start End Name Score Strand 0 chr1 65537 65538 a 0 - 1 chr1 65537 65538 a 0 - 2 chr1 65537 65538 a 0 - 3 chr1 65537 65538 a 0 - 4 chr1 65537 65538 a 0 - 5 chr4 65537 65538 a 0 - 6 chr21 7 8 a 0 - 7 chr22 65537 65794 a 0 - Chromosome Start End Name Score Strand 0 chr1 8 12 a 0 - 1 chr1 8 11 a 0 - 2 chr1 8 11 a 0 - 3 chr1 7 10 a 0 - 4 chr1 8 11 a 0 - 5 chr1 8 11 a 0 - 6 chr19 8 11 a 0 - 7 chrM 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmphws7fut6/f1.bed -b /tmp/tmphws7fut6/f2.bed Chromosome Start End Name Score Strand 0 chr1 65537 65538 a 0 - 1 chr1 65537 65538 a 0 - 2 chr1 65537 65538 a 0 - 3 chr1 65537 65538 a 0 - 4 chr1 65537 65538 a 0 - 5 chr4 65537 65538 a 0 - 6 chr21 7 8 a 0 - 7 chrM 65537 65794 a 0 - Chromosome Start End Name Score Strand 0 chr1 8 12 a 0 - 1 chr1 8 11 a 0 - 2 chr1 8 11 a 0 - 3 chr1 7 10 a 0 - 4 chr1 8 11 a 0 - 5 chr1 8 11 a 0 - 6 chr19 8 11 a 0 - 7 chrM 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpxq14gk8z/f1.bed -b /tmp/tmpxq14gk8z/f2.bed Chromosome Start End Name Score Strand 0 chr1 8 12 a 0 - 1 chr1 8 11 a 0 - 2 chr1 8 11 a 0 - 3 chr1 7 10 a 0 - 4 chr1 8 11 a 0 - 5 chr1 8 11 a 0 - 6 chr19 8 11 a 0 - 7 chrM 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 8 12 a 0 - 1 chr1 8 11 a 0 - 2 chr1 8 11 a 0 - 3 chr1 7 10 a 0 - 4 chr1 8 11 a 0 - 5 chr1 8 11 a 0 - 6 chr19 8 11 a 0 - 7 chrM 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpdpf_sgvb/f1.bed -b /tmp/tmpdpf_sgvb/f2.bed Chromosome Start End Name Score Strand 0 chr1 8 12 a 0 - 1 chr1 8 11 a 0 - 2 chr1 8 11 a 0 - 3 chr1 7 10 a 0 - 4 chr1 8 11 a 0 - 5 chr1 8 11 a 0 - 6 chr19 8 11 a 0 - 7 chrM 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 8 12 a 0 - 1 chr1 8 11 a 0 - 2 chr1 8 11 a 0 - 3 chr1 7 10 a 0 - 4 chr1 8 11 a 0 - 5 chr19 8 11 a 0 - 6 chrM 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpf1leoosf/f1.bed -b /tmp/tmpf1leoosf/f2.bed Chromosome Start End Name Score Strand 0 chr13 2104711 2107789 a 0 - Chromosome Start End Name Score Strand 0 chr1 641020 649847 a 0 + 1 chr1 3047899 3050982 a 0 + 2 chr1 10000000 10001859 a 0 - 3 chr1 3861311 3863836 a 0 - 4 chr9 8676818 8683564 a 0 - 5 chr13 4275169 4276820 a 0 - 6 chr18 6727222 6735378 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp5pigs1k1/f1.bed -b /tmp/tmp5pigs1k1/f2.bed Chromosome Start End Name Score Strand 0 chr13 2104711 2107789 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 9896 a 0 + 1 chr1 10000000 10009895 a 0 + 2 chr1 1 9896 a 0 + 3 chr1 4 261 a 0 - 4 chr9 5 9900 a 0 + 5 chr13 1 258 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpv42h32qq/f1.bed -b /tmp/tmpv42h32qq/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp59szzfvh/f1.bed -b /tmp/tmp59szzfvh/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmplx_yc8i_/f1.bed -b /tmp/tmplx_yc8i_/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpp0eb9oye/f1.bed -b /tmp/tmpp0eb9oye/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpxa4uhhmp/f1.bed -b /tmp/tmpxa4uhhmp/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp6n4x1vnc/f1.bed -b /tmp/tmp6n4x1vnc/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp7v0fuy2z/f1.bed -b /tmp/tmp7v0fuy2z/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp36dh6577/f1.bed -b /tmp/tmp36dh6577/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpa0l79u1h/f1.bed -b /tmp/tmpa0l79u1h/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 8841759 8845640 a 0 + 1 chr1 1 3882 a 0 + 2 chr1 4178067 4181948 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp79wktupt/f1.bed -b /tmp/tmp79wktupt/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpw2a2_otq/f1.bed -b /tmp/tmpw2a2_otq/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr3 8407540 8411599 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpxvw6oz69/f1.bed -b /tmp/tmpxvw6oz69/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpxq4_2gyp/f1.bed -b /tmp/tmpxq4_2gyp/f2.bed Chromosome Start End Name Score Strand 0 chr11 1 2 a 0 + 1 chr11 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 3987984 3996020 a 0 + 1 chr1 1199949 1200829 a 0 + 2 chr5 1199949 1207477 a 0 + 3 chr8 1199949 1209932 a 0 + 4 chr14 1199949 1200844 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmppz16m5xj/f1.bed -b /tmp/tmppz16m5xj/f2.bed Chromosome Start End Name Score Strand 0 chr11 1 2 a 0 + 1 chr11 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpyc2hap95/f1.bed -b /tmp/tmpyc2hap95/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr2 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 4677471 4685398 a 0 - 1 chr6 1185953 1186405 a 0 - 2 chr13 3678524 3681596 a 0 - 3 chr21 1296062 1306027 a 0 - 4 chr22 8419324 8428549 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmprw76jcdr/f1.bed -b /tmp/tmprw76jcdr/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr2 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpjmp6lyto/f1.bed -b /tmp/tmpjmp6lyto/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 8006982 8009779 a 0 - 1 chr17 2344379 2351608 a 0 - 2 chr21 1 7738 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp8odeasqs/f1.bed -b /tmp/tmp8odeasqs/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp1wwmn94e/f1.bed -b /tmp/tmp1wwmn94e/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 7794427 7794633 a 0 + 1 chr1 6035519 6039408 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp891ay88q/f1.bed -b /tmp/tmp891ay88q/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpotjwyfnt/f1.bed -b /tmp/tmpotjwyfnt/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 9628673 9628674 a 0 - 1 chrY 3575806 3577134 a 0 + 2 chrY 7409932 7419146 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpnpdoj3qs/f1.bed -b /tmp/tmpnpdoj3qs/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpqvxpv8f5/f1.bed -b /tmp/tmpqvxpv8f5/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 3749689 3754117 a 0 + 1 chr1 1010387 1019901 a 0 + 2 chr1 1145436 1154950 a 0 + 3 chr1 8732566 8742080 a 0 + 4 chr1 5544465 5553979 a 0 - 5 chr1 3234624 3244138 a 0 - 6 chr1 7561481 7570995 a 0 - 7 chr15 3598604 3602482 a 0 + 8 chr15 7887031 7894786 a 0 - 9 chrM 7887031 7896545 a 0 - 10 chrY 7887031 7897031 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpxa6e1wag/f1.bed -b /tmp/tmpxa6e1wag/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp9acy40rs/f1.bed -b /tmp/tmp9acy40rs/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 8216088 8219729 a 0 + 1 chr1 2742934 2752934 a 0 + 2 chr1 171921 180463 a 0 + 3 chr1 7511541 7516374 a 0 + 4 chr5 3801256 3811256 a 0 + 5 chrY 4934478 4944478 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpuyhyog79/f1.bed -b /tmp/tmpuyhyog79/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpx1yji6lv/f1.bed -b /tmp/tmpx1yji6lv/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 824637 833158 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp0mxzwjzk/f1.bed -b /tmp/tmp0mxzwjzk/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpdqfprdpq/f1.bed -b /tmp/tmpdqfprdpq/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 6720002 6727223 a 0 + 1 chr1 7605260 7612944 a 0 + 2 chr1 33800 40615 a 0 + 3 chr1 3509846 3518981 a 0 + 4 chr1 327194 329795 a 0 - 5 chr1 6191223 6195413 a 0 - 6 chr1 9999999 10001143 a 0 - 7 chr3 8293706 8294297 a 0 + 8 chr3 6191223 6192966 a 0 - 9 chr15 5558434 5561053 a 0 - 10 chrM 3237828 3247102 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp74br3jso/f1.bed -b /tmp/tmp74br3jso/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp7kz10hp4/f1.bed -b /tmp/tmp7kz10hp4/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 2106912 2114013 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp_i6p2x9p/f1.bed -b /tmp/tmp_i6p2x9p/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp3y0s57ic/f1.bed -b /tmp/tmp3y0s57ic/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 7486673 7493079 a 0 + 1 chr1 866503 871920 a 0 + 2 chr1 9748792 9755003 a 0 - 3 chr6 6732964 6735406 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp8e2k2tmi/f1.bed -b /tmp/tmp8e2k2tmi/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpzbbw0jjw/f1.bed -b /tmp/tmpzbbw0jjw/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 7707517 7716743 a 0 + 1 chr1 638611 648611 a 0 + 2 chr1 5536273 5545538 a 0 + 3 chr1 6787210 6788412 a 0 + 4 chr1 4296770 4297886 a 0 - 5 chr1 1536321 1544484 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmptc3imjw9/f1.bed -b /tmp/tmptc3imjw9/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp4ytl_b6b/f1.bed -b /tmp/tmp4ytl_b6b/f2.bed Chromosome Start End Name Score Strand 0 chr8 9325226 9325227 a 0 + Chromosome Start End Name Score Strand 0 chr1 244 3357 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp48pmhjbw/f1.bed -b /tmp/tmp48pmhjbw/f2.bed Chromosome Start End Name Score Strand 0 chr8 9325226 9325227 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp6r95p4ms/f1.bed -b /tmp/tmp6r95p4ms/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr2 8273388 8279806 a 0 + 1 chr14 8536257 8543269 a 0 + 2 chr15 7349272 7353357 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpvyf02c3b/f1.bed -b /tmp/tmpvyf02c3b/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpgyvcgxk9/f1.bed -b /tmp/tmpgyvcgxk9/f2.bed Chromosome Start End Name Score Strand 0 chr4 1274297 1274298 a 0 + Chromosome Start End Name Score Strand 0 chr1 46 5364 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpayiazfou/f1.bed -b /tmp/tmpayiazfou/f2.bed Chromosome Start End Name Score Strand 0 chr4 1274297 1274298 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpzf8le8bj/f1.bed -b /tmp/tmpzf8le8bj/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 2570924 2572940 a 0 + 1 chr1 4492593 4501775 a 0 + 2 chr1 1520722 1526281 a 0 - 3 chr1 5587502 5592331 a 0 - 4 chr1 6586499 6588874 a 0 - 5 chr1 977908 987417 a 0 - 6 chrY 5247243 5249670 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmprffmw3rn/f1.bed -b /tmp/tmprffmw3rn/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp5zpz43rr/f1.bed -b /tmp/tmp5zpz43rr/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 47474 50044 a 0 - 1 chr1 5044993 5052559 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpbb7nuld7/f1.bed -b /tmp/tmpbb7nuld7/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpoh5i7rtx/f1.bed -b /tmp/tmpoh5i7rtx/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 6116490 6124890 a 0 - 1 chr1 285796 286661 a 0 - 2 chr1 6958253 6959139 a 0 - 3 chr10 3250899 3254690 a 0 + 4 chr22 3329667 3332598 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp2bgnwz4n/f1.bed -b /tmp/tmp2bgnwz4n/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpxawpgsp6/f1.bed -b /tmp/tmpxawpgsp6/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 5263850 5268975 a 0 + 1 chr1 9999999 10009804 a 0 - 2 chr2 1600187 1607097 a 0 + 3 chr2 9999999 10001819 a 0 + 4 chr6 8491957 8498894 a 0 + 5 chr16 9999999 10009696 a 0 + 6 chr16 9999999 10008003 a 0 - 7 chr20 9999999 10000366 a 0 + 8 chrX 7789200 7790119 a 0 - 9 chrY 8808447 8817990 a 0 + 10 chrY 8835232 8842333 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp74hcsooe/f1.bed -b /tmp/tmp74hcsooe/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpig53tyew/f1.bed -b /tmp/tmpig53tyew/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr14 4755337 4759105 a 0 + 1 chr14 9649017 9649067 a 0 - 2 chr14 5934900 5935398 a 0 - 3 chr14 6953167 6954958 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpzs9wkouo/f1.bed -b /tmp/tmpzs9wkouo/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpswkiqb4a/f1.bed -b /tmp/tmpswkiqb4a/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr3 2111596 2114235 a 0 + 1 chr6 2603920 2612760 a 0 + 2 chr6 1039586 1044771 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp_i5i26x1/f1.bed -b /tmp/tmp_i5i26x1/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp0bzd8yqv/f1.bed -b /tmp/tmp0bzd8yqv/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 4954175 4959979 a 0 + 1 chr1 4954175 4961767 a 0 + 2 chr1 4954175 4963731 a 0 - 3 chr1 4954175 4964163 a 0 - 4 chr1 4954175 4962064 a 0 - 5 chr8 4954175 4961013 a 0 + 6 chr10 4954175 4962606 a 0 + 7 chr15 4954175 4958253 a 0 - 8 chr17 4954175 4954176 a 0 - 9 chr19 4954175 4961013 a 0 + 10 chr19 4954175 4958802 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp99rnunyw/f1.bed -b /tmp/tmp99rnunyw/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp95_pwj5o/f1.bed -b /tmp/tmp95_pwj5o/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr3 4339795 4341680 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpx0gk51l0/f1.bed -b /tmp/tmpx0gk51l0/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmppr6vr069/f1.bed -b /tmp/tmppr6vr069/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 7178100 7186034 a 0 - 1 chr9 9785578 9791655 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpugunf1bj/f1.bed -b /tmp/tmpugunf1bj/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpbx93rppr/f1.bed -b /tmp/tmpbx93rppr/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + 4 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 8108460 8116455 a 0 + 1 chr1 1 3 a 0 + 2 chr2 1 725 a 0 - 3 chr14 1 7157 a 0 - 4 chr18 504623 505710 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp47o5l2u5/f1.bed -b /tmp/tmp47o5l2u5/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + 4 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpgz8lfjju/f1.bed -b /tmp/tmpgz8lfjju/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 8307778 8315918 a 0 + 1 chr1 2283509 2283510 a 0 + 2 chr1 1731789 1741789 a 0 + 3 chr1 5307257 5307841 a 0 + 4 chr1 5322981 5332739 a 0 - 5 chr1 3154235 3156722 a 0 - 6 chr1 4062407 4068748 a 0 - 7 chr1 3154235 3154236 a 0 - 8 chr1 5241297 5251023 a 0 - 9 chr10 2 8154 a 0 - 10 chr19 5355154 5355502 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmphx8r3k54/f1.bed -b /tmp/tmphx8r3k54/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpxdhgw7gc/f1.bed -b /tmp/tmpxdhgw7gc/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 5075024 5082240 a 0 + 1 chr1 10000000 10007385 a 0 + 2 chr1 5632899 5640591 a 0 + 3 chr1 8360279 8360280 a 0 + 4 chr1 7132977 7138516 a 0 + 5 chr1 1810074 1815481 a 0 - 6 chr1 4160981 4166437 a 0 - 7 chr3 7767015 7771124 a 0 + 8 chr6 8281243 8290640 a 0 - 9 chr14 9733977 9734080 a 0 - 10 chr15 4119809 4127056 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmph7ue_hiv/f1.bed -b /tmp/tmph7ue_hiv/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp4ay3omlx/f1.bed -b /tmp/tmp4ay3omlx/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr19 5533645 5539489 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpuwvpvqou/f1.bed -b /tmp/tmpuwvpvqou/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmps03bf435/f1.bed -b /tmp/tmps03bf435/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 2419526 2423003 a 0 + 1 chr1 5829897 5834665 a 0 - 2 chr1 5829897 5832148 a 0 - 3 chr1 5829897 5834665 a 0 - 4 chr14 5829897 5839830 a 0 + 5 chrM 5829897 5834665 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp1ddq91eq/f1.bed -b /tmp/tmp1ddq91eq/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpoi7dhagh/f1.bed -b /tmp/tmpoi7dhagh/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 5071057 5079851 a 0 + 1 chr11 5157650 5166827 a 0 - 2 chr22 4019987 4027214 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmppw1kag3b/f1.bed -b /tmp/tmppw1kag3b/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpfs4285rv/f1.bed -b /tmp/tmpfs4285rv/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1623313 1632368 a 0 + 1 chr1 1623313 1624503 a 0 - 2 chr1 1623313 1628357 a 0 - 3 chr1 5640473 5643725 a 0 - 4 chr7 1623313 1625664 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpt8xrgjz1/f1.bed -b /tmp/tmpt8xrgjz1/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpulvmigfs/f1.bed -b /tmp/tmpulvmigfs/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + 4 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 9809035 9811658 a 0 + 1 chr1 2228458 2228747 a 0 - 2 chr3 1074174 1076797 a 0 - 3 chr5 1074174 1083967 a 0 + 4 chr14 3013127 3015743 a 0 + 5 chr16 1074174 1080626 a 0 + 6 chr16 2483260 2485883 a 0 - 7 chr16 6280706 6283329 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp2c1ju1il/f1.bed -b /tmp/tmp2c1ju1il/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + 4 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpxgt310yb/f1.bed -b /tmp/tmpxgt310yb/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 8073506 8077756 a 0 + 1 chr1 8217500 8219255 a 0 + 2 chr1 4786782 4790133 a 0 + 3 chr1 4066236 4075453 a 0 + 4 chr1 10000000 10003385 a 0 + 5 chr4 2768405 2768407 a 0 - 6 chr10 3676430 3685034 a 0 - 7 chr11 4786782 4788816 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp5_j5jlgg/f1.bed -b /tmp/tmp5_j5jlgg/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmprcvxf64a/f1.bed -b /tmp/tmprcvxf64a/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 4102128 4102130 a 0 + 1 chr17 8902755 8912481 a 0 + 2 chr21 7936908 7938441 a 0 + 3 chr22 7038550 7043809 a 0 + 4 chr22 10000000 10008578 a 0 + 5 chr22 5786137 5789927 a 0 + 6 chr22 3299349 3301863 a 0 - 7 chr22 9712898 9717463 a 0 - 8 chr22 9230277 9233941 a 0 - 9 chr22 9111851 9118447 a 0 - 10 chrY 6193096 6196204 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmplxkviy92/f1.bed -b /tmp/tmplxkviy92/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp31zz2hzv/f1.bed -b /tmp/tmp31zz2hzv/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + 4 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 62172 63783 a 0 + 1 chr1 1 3056 a 0 + 2 chr1 955592 958208 a 0 - 3 chr1 5283332 5291264 a 0 - 4 chr1 7667873 7674317 a 0 - 5 chr1 787639 795828 a 0 - 6 chr9 2587813 2596960 a 0 + 7 chr10 8421381 8428424 a 0 + 8 chr10 9999999 10007267 a 0 - 9 chr12 8375857 8383946 a 0 + 10 chr22 9933297 9936173 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpiy8be1j9/f1.bed -b /tmp/tmpiy8be1j9/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + 4 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpvmscomo3/f1.bed -b /tmp/tmpvmscomo3/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 5431044 5436570 a 0 - 1 chr1 2602170 2611177 a 0 - 2 chr1 9654681 9660207 a 0 - 3 chr1 6952772 6958298 a 0 - 4 chr3 745142 750668 a 0 - 5 chr11 1246940 1252466 a 0 + 6 chr11 3177459 3182985 a 0 - 7 chr16 5003536 5008656 a 0 + 8 chr22 2784178 2789704 a 0 + 9 chrM 2789984 2795510 a 0 + 10 chrX 5320741 5322621 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpknz4eg1t/f1.bed -b /tmp/tmpknz4eg1t/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpd6skz92q/f1.bed -b /tmp/tmpd6skz92q/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr6 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 3148019 3155214 a 0 + 1 chr16 3148019 3157357 a 0 - 2 chrX 3148019 3150043 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpzz4w7jz7/f1.bed -b /tmp/tmpzz4w7jz7/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr6 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp0q68b_5y/f1.bed -b /tmp/tmp0q68b_5y/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 9843412 9847418 a 0 + 1 chr1 9843412 9847418 a 0 + 2 chr1 3379555 3383561 a 0 + 3 chr1 7834974 7838980 a 0 + 4 chr1 7659377 7663383 a 0 + 5 chr1 9843412 9847418 a 0 + 6 chr1 9843412 9850419 a 0 + 7 chr1 5917640 5921646 a 0 + 8 chr1 9843412 9847418 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp1tz4ka_q/f1.bed -b /tmp/tmp1tz4ka_q/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpdji86x4d/f1.bed -b /tmp/tmpdji86x4d/f2.bed Chromosome Start End Name Score Strand 0 chr1 8061185 8061186 a 0 + Chromosome Start End Name Score Strand 0 chr1 3043287 3048568 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpklwdaksc/f1.bed -b /tmp/tmpklwdaksc/f2.bed Chromosome Start End Name Score Strand 0 chr1 8061185 8061186 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp0y_shv_s/f1.bed -b /tmp/tmp0y_shv_s/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 7108277 7113996 a 0 - 1 chr1 1820992 1823084 a 0 - 2 chr1 4771461 4774205 a 0 - 3 chr9 2442074 2452073 a 0 + 4 chr11 3330783 3340087 a 0 + 5 chr11 4670089 4673393 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpeg3kak96/f1.bed -b /tmp/tmpeg3kak96/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmps_9re7es/f1.bed -b /tmp/tmps_9re7es/f2.bed Chromosome Start End Name Score Strand 0 chr10 1041669 1041926 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 3889 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp_5p73bqg/f1.bed -b /tmp/tmp_5p73bqg/f2.bed Chromosome Start End Name Score Strand 0 chr10 1041669 1041926 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmphcfx7s9w/f1.bed -b /tmp/tmphcfx7s9w/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 5360941 5360949 a 0 + 1 chr1 7886720 7891217 a 0 + 2 chr1 5935416 5944830 a 0 + 3 chr1 328056 333442 a 0 + 4 chr1 3050993 3055309 a 0 - 5 chr1 9288172 9296236 a 0 - 6 chr8 5793434 5801653 a 0 + 7 chr14 7931206 7931482 a 0 + 8 chr17 4372997 4373867 a 0 + 9 chr21 978208 986011 a 0 + 10 chrM 5360941 5370832 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpnnymk5_w/f1.bed -b /tmp/tmpnnymk5_w/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpod9j1b29/f1.bed -b /tmp/tmpod9j1b29/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 3183479 3185058 a 0 + 1 chr1 6236379 6237958 a 0 + 2 chr1 6648025 6648026 a 0 + 3 chr1 6557890 6560329 a 0 + 4 chr1 313971 317201 a 0 - 5 chr7 114466 116468 a 0 - 6 chr8 4178018 4180250 a 0 - 7 chr8 2521088 2530364 a 0 - 8 chr13 2975209 2978284 a 0 - 9 chr16 6519706 6524166 a 0 - 10 chr17 150829 159067 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpgdciladc/f1.bed -b /tmp/tmpgdciladc/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp8m62wu3u/f1.bed -b /tmp/tmp8m62wu3u/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr13 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 7257829 7265364 a 0 + 1 chr1 7090895 7096635 a 0 + 2 chr10 7100594 7106221 a 0 + 3 chr10 3527069 3527469 a 0 + 4 chr10 10000000 10008181 a 0 + 5 chr10 524135 526970 a 0 - 6 chr10 5541102 5545441 a 0 - 7 chr10 3183359 3183580 a 0 - 8 chr10 3041689 3047507 a 0 - 9 chr21 4938968 4939368 a 0 - 10 chrM 8296804 8297204 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpdy7udt9z/f1.bed -b /tmp/tmpdy7udt9z/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr13 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp24h5ehsi/f1.bed -b /tmp/tmp24h5ehsi/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 8390573 8394994 a 0 + 1 chr1 4393748 4397334 a 0 + 2 chr1 5973052 5982098 a 0 + 3 chr1 7873381 7877700 a 0 + 4 chr8 6743744 6753319 a 0 - 5 chrX 4724916 4726676 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp2df0oxr4/f1.bed -b /tmp/tmp2df0oxr4/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpzaxq23d8/f1.bed -b /tmp/tmpzaxq23d8/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1559000 1563196 a 0 + 1 chr1 3296059 3305809 a 0 + 2 chr1 5042515 5051764 a 0 + 3 chr1 2646487 2650286 a 0 - 4 chr1 279723 279767 a 0 - 5 chr8 6043521 6046825 a 0 + 6 chr11 2758934 2764987 a 0 + 7 chr18 7965163 7969645 a 0 - 8 chr19 3233030 3241967 a 0 - 9 chrM 1722599 1723543 a 0 + 10 chrY 1909380 1919360 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpxcylys5x/f1.bed -b /tmp/tmpxcylys5x/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpbu8qemkg/f1.bed -b /tmp/tmpbu8qemkg/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 4869801 4870542 a 0 + 1 chr1 3891425 3895060 a 0 + 2 chr1 8545526 8545805 a 0 + 3 chr1 9279663 9279976 a 0 + 4 chr1 9279663 9287870 a 0 - 5 chr1 9279663 9287953 a 0 - 6 chr1 9279663 9283472 a 0 - 7 chr4 9279663 9284367 a 0 - 8 chr5 9279663 9288279 a 0 + 9 chr11 6416657 6423976 a 0 + 10 chr15 9279663 9289492 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpg3q1wclt/f1.bed -b /tmp/tmpg3q1wclt/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmplhvy3gus/f1.bed -b /tmp/tmplhvy3gus/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 6978778 6978807 a 0 + 1 chr1 8581244 8583849 a 0 + 2 chr1 685751 693091 a 0 - 3 chr1 6823073 6828945 a 0 - 4 chr1 2 2975 a 0 - 5 chr1 742097 746832 a 0 - 6 chr1 6764594 6770466 a 0 - 7 chr1 9686707 9692579 a 0 - 8 chr21 5123058 5128930 a 0 + 9 chr21 601145 609287 a 0 - 10 chrX 6746255 6750156 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp9w_diaf8/f1.bed -b /tmp/tmp9w_diaf8/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpihl2jz_7/f1.bed -b /tmp/tmpihl2jz_7/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 5411415 5417262 a 0 + 1 chr1 4370925 4378522 a 0 + 2 chr1 1355133 1357357 a 0 - 3 chr7 8680407 8682973 a 0 + 4 chr7 3851340 3858856 a 0 + 5 chr13 9630720 9630841 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmplg0ny2ak/f1.bed -b /tmp/tmplg0ny2ak/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpckphm0n0/f1.bed -b /tmp/tmpckphm0n0/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr21 6151854 6157419 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpnamexv0_/f1.bed -b /tmp/tmpnamexv0_/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp2hhkl5zu/f1.bed -b /tmp/tmp2hhkl5zu/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 9604070 9610879 a 0 + 1 chr1 5497628 5505803 a 0 + 2 chr1 9999999 10005091 a 0 + 3 chr1 2551868 2555588 a 0 + 4 chr1 1010895 1014269 a 0 + 5 chr1 2992505 2996245 a 0 + 6 chr11 7009001 7014864 a 0 + 7 chr14 5373576 5383277 a 0 + 8 chr14 4724119 4733912 a 0 + 9 chr14 9854699 9857313 a 0 - 10 chr17 3588414 3598414 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp1bezhjff/f1.bed -b /tmp/tmp1bezhjff/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmprtaovops/f1.bed -b /tmp/tmprtaovops/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 5120766 5128928 a 0 - 1 chr1 8426790 8429740 a 0 - 2 chr17 1902673 1908464 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpzwewwq7m/f1.bed -b /tmp/tmpzwewwq7m/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpmroucz75/f1.bed -b /tmp/tmpmroucz75/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr6 8587081 8594856 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp5rei6zpq/f1.bed -b /tmp/tmp5rei6zpq/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpxct0dm2p/f1.bed -b /tmp/tmpxct0dm2p/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 5262434 5269782 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpbmbkpkr3/f1.bed -b /tmp/tmpbmbkpkr3/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpnq4s2167/f1.bed -b /tmp/tmpnq4s2167/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 3880264 3890264 a 0 + 1 chr10 3880264 3888960 a 0 - 2 chr12 3880264 3888960 a 0 - 3 chr21 3880264 3888960 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp7444q9_f/f1.bed -b /tmp/tmp7444q9_f/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpt250m_5j/f1.bed -b /tmp/tmpt250m_5j/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1565171 1569553 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp6vs2_onw/f1.bed -b /tmp/tmp6vs2_onw/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp8nmmek6o/f1.bed -b /tmp/tmp8nmmek6o/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr3 4919738 4924579 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp8y4vg6zt/f1.bed -b /tmp/tmp8y4vg6zt/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpihja_bqe/f1.bed -b /tmp/tmpihja_bqe/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1503756 1513756 a 0 + 1 chr1 1992337 2002337 a 0 + 2 chr1 2436164 2446164 a 0 + 3 chr1 4362151 4372151 a 0 + 4 chr1 8546891 8556891 a 0 + 5 chr1 5767248 5777248 a 0 - 6 chr7 9936166 9946166 a 0 - 7 chr9 1821740 1831740 a 0 - 8 chr10 9313548 9323548 a 0 + 9 chr17 3163258 3173258 a 0 - 10 chrX 5884944 5894944 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpctej3udn/f1.bed -b /tmp/tmpctej3udn/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpl0gtmqev/f1.bed -b /tmp/tmpl0gtmqev/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 7446980 7452965 a 0 + 1 chr1 2821029 2824564 a 0 + 2 chr1 7280852 7283355 a 0 - 3 chr1 4973623 4979760 a 0 - 4 chr13 6843104 6844445 a 0 - 5 chr16 6120662 6120808 a 0 + 6 chr16 2616289 2626288 a 0 - 7 chr18 7191085 7194918 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp9b3jjyx8/f1.bed -b /tmp/tmp9b3jjyx8/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpae09eace/f1.bed -b /tmp/tmpae09eace/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 8675044 8680331 a 0 + 1 chr1 8675044 8680331 a 0 + 2 chr9 8675044 8680331 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpr14524kr/f1.bed -b /tmp/tmpr14524kr/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpgx886jj9/f1.bed -b /tmp/tmpgx886jj9/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr16 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 2161389 2171341 a 0 + 1 chr1 3539338 3543014 a 0 - 2 chr20 4747479 4754264 a 0 + 3 chr20 7968580 7972256 a 0 - 4 chr21 2799449 2809449 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpukiphi2m/f1.bed -b /tmp/tmpukiphi2m/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr16 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpy2eqpbj6/f1.bed -b /tmp/tmpy2eqpbj6/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr2 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 105245 114507 a 0 + 1 chr1 1537629 1539166 a 0 + 2 chr1 1813063 1822809 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp_sn3gchq/f1.bed -b /tmp/tmp_sn3gchq/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr2 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp26p9dkx_/f1.bed -b /tmp/tmp26p9dkx_/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 3010144 3011038 a 0 + 1 chr1 2959181 2959197 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp9xtjxcon/f1.bed -b /tmp/tmp9xtjxcon/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpskel9rj6/f1.bed -b /tmp/tmpskel9rj6/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chrY 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 605184 607566 a 0 + 1 chr1 830184 838515 a 0 + 2 chr1 2087142 2093978 a 0 + 3 chr1 3028569 3034226 a 0 - 4 chr1 3028569 3034945 a 0 - 5 chr1 7058363 7061947 a 0 - 6 chr1 3028569 3037957 a 0 - 7 chr1 8542864 8549790 a 0 - 8 chr4 2933571 2938946 a 0 + 9 chr11 3028569 3030331 a 0 - 10 chr21 7432037 7435457 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpzv72bx75/f1.bed -b /tmp/tmpzv72bx75/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chrY 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpm755z6ak/f1.bed -b /tmp/tmpm755z6ak/f2.bed Chromosome Start End Name Score Strand 0 chr16 5584984 5584985 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 8612 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmps7lhz0la/f1.bed -b /tmp/tmps7lhz0la/f2.bed Chromosome Start End Name Score Strand 0 chr16 5584984 5584985 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp7dq8mcwx/f1.bed -b /tmp/tmp7dq8mcwx/f2.bed Chromosome Start End Name Score Strand 0 chr1 2390198 2390199 a 0 + Chromosome Start End Name Score Strand 0 chr1 47 2099 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpiqufituq/f1.bed -b /tmp/tmpiqufituq/f2.bed Chromosome Start End Name Score Strand 0 chr1 2390198 2390199 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpco56g1bn/f1.bed -b /tmp/tmpco56g1bn/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 7373642 7373643 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpptvj9u9o/f1.bed -b /tmp/tmpptvj9u9o/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpec54z5tu/f1.bed -b /tmp/tmpec54z5tu/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr16 3160161 3160205 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpoph2rhut/f1.bed -b /tmp/tmpoph2rhut/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpm0z95uva/f1.bed -b /tmp/tmpm0z95uva/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + 4 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 7126618 7133033 a 0 + 1 chr1 5532270 5534288 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmppwujmc_5/f1.bed -b /tmp/tmppwujmc_5/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + 4 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpzqaun6ur/f1.bed -b /tmp/tmpzqaun6ur/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 2380534 2389806 a 0 + 1 chr11 10000000 10008945 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpvna9a4sl/f1.bed -b /tmp/tmpvna9a4sl/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp8fsw4w2p/f1.bed -b /tmp/tmp8fsw4w2p/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 8583616 8590954 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpchgpcbfm/f1.bed -b /tmp/tmpchgpcbfm/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp2cokn2m6/f1.bed -b /tmp/tmp2cokn2m6/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 2902378 2909240 a 0 + 1 chr1 8147361 8155059 a 0 + 2 chr1 3959510 3967981 a 0 + 3 chr1 5266414 5274692 a 0 + 4 chr1 2326875 2330131 a 0 + 5 chr1 2902378 2907359 a 0 + 6 chr1 1958884 1967267 a 0 + 7 chr6 2902378 2908130 a 0 - 8 chr7 874575 882724 a 0 - 9 chr14 2902378 2904832 a 0 + 10 chrX 6814309 6818617 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpsy5_676x/f1.bed -b /tmp/tmpsy5_676x/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpazfw72dq/f1.bed -b /tmp/tmpazfw72dq/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + 4 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 624307 629552 a 0 + 1 chr1 5047865 5053344 a 0 + 2 chr1 1602284 1602373 a 0 + 3 chr1 4154282 4154358 a 0 + 4 chr1 9032250 9035329 a 0 + 5 chr1 2048605 2055283 a 0 - 6 chr1 6498057 6503262 a 0 - 7 chr14 7864830 7868192 a 0 - 8 chr15 8110931 8118875 a 0 + 9 chrY 6130693 6138775 a 0 + 10 chrY 3298958 3307026 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmptpr2xkys/f1.bed -b /tmp/tmptpr2xkys/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + 4 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp5pp1rn27/f1.bed -b /tmp/tmp5pp1rn27/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr7 2342591 2346619 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp6qjok0i4/f1.bed -b /tmp/tmp6qjok0i4/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmprur3wifm/f1.bed -b /tmp/tmprur3wifm/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 8378494 8379884 a 0 + 1 chr1 10000000 10007574 a 0 + 2 chr1 10000000 10008356 a 0 - 3 chr1 9005723 9006533 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmptp9fpier/f1.bed -b /tmp/tmptp9fpier/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp5ynvlvox/f1.bed -b /tmp/tmp5ynvlvox/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr14 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 8724883 8726847 a 0 + 1 chr1 8724883 8730811 a 0 - 2 chr1 8724883 8727187 a 0 - 3 chr4 9175527 9178058 a 0 - 4 chr18 504381 510875 a 0 - 5 chr19 6695026 6704695 a 0 + 6 chr20 8724883 8731377 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpr_b4excy/f1.bed -b /tmp/tmpr_b4excy/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr14 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpvcggf244/f1.bed -b /tmp/tmpvcggf244/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 5117083 5123002 a 0 + 1 chr1 7050243 7050244 a 0 + 2 chr1 4572435 4579630 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpj3mcbd1u/f1.bed -b /tmp/tmpj3mcbd1u/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp7xrnlvlx/f1.bed -b /tmp/tmp7xrnlvlx/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 988141 995036 a 0 + 1 chr1 2964463 2972696 a 0 + 2 chr1 6959560 6964451 a 0 - 3 chr1 1993974 2003658 a 0 - 4 chr1 5758193 5766696 a 0 - 5 chr1 5590407 5593808 a 0 - 6 chr2 2964463 2964698 a 0 - 7 chr6 5734839 5744839 a 0 + 8 chr11 6560288 6563324 a 0 - 9 chr16 2964463 2970355 a 0 + 10 chr18 1633642 1641193 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpeaoban9c/f1.bed -b /tmp/tmpeaoban9c/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpg_1iji5y/f1.bed -b /tmp/tmpg_1iji5y/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 7389788 7390687 a 0 + 1 chr1 2028617 2028618 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpxwyc7r8s/f1.bed -b /tmp/tmpxwyc7r8s/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpk35a29qi/f1.bed -b /tmp/tmpk35a29qi/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 9302038 9305733 a 0 + 1 chr1 2912355 2912592 a 0 - 2 chr1 9999999 10005978 a 0 - 3 chr1 6398980 6403364 a 0 - 4 chr2 1021674 1028171 a 0 + 5 chr5 6398980 6399821 a 0 + 6 chr7 359070 364501 a 0 + 7 chr11 6158451 6158452 a 0 - 8 chr19 6398980 6400346 a 0 + 9 chr22 1213998 1217571 a 0 + 10 chrM 7597502 7601613 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmplstild6s/f1.bed -b /tmp/tmplstild6s/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpq0hb5ogs/f1.bed -b /tmp/tmpq0hb5ogs/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2307 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 9589 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp_wz4tf6d/f1.bed -b /tmp/tmp_wz4tf6d/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2307 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpbi6h5ur8/f1.bed -b /tmp/tmpbi6h5ur8/f2.bed Chromosome Start End Name Score Strand 0 chr1 9202640 9202641 a 0 + Chromosome Start End Name Score Strand 0 chr1 29 6986 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp2o33lrjm/f1.bed -b /tmp/tmp2o33lrjm/f2.bed Chromosome Start End Name Score Strand 0 chr1 9202640 9202641 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpk8u_ko18/f1.bed -b /tmp/tmpk8u_ko18/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr10 1552483 1556771 a 0 - 1 chr15 8409197 8409991 a 0 + 2 chr18 1 1623 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmph9uima26/f1.bed -b /tmp/tmph9uima26/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp1tjmunbi/f1.bed -b /tmp/tmp1tjmunbi/f2.bed Chromosome Start End Name Score Strand 0 chr1 9975555 9975556 a 0 + Chromosome Start End Name Score Strand 0 chr1 60455 64636 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmphuh1fjwa/f1.bed -b /tmp/tmphuh1fjwa/f2.bed Chromosome Start End Name Score Strand 0 chr1 9975555 9975556 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp2ub2ygnh/f1.bed -b /tmp/tmp2ub2ygnh/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr2 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 3223701 3230355 a 0 + 1 chr22 3149249 3157415 a 0 + 2 chr22 8267552 8275086 a 0 + 3 chr22 1824323 1825078 a 0 - 4 chr22 10000000 10010000 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp8r6o2kkq/f1.bed -b /tmp/tmp8r6o2kkq/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr2 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp5n5_535w/f1.bed -b /tmp/tmp5n5_535w/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr3 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 6621697 6623412 a 0 + 1 chr1 9888937 9898254 a 0 + 2 chr1 4606158 4607338 a 0 - 3 chr1 3073162 3080271 a 0 - 4 chr2 3060958 3068067 a 0 + 5 chr2 7183721 7189763 a 0 + 6 chr8 2472045 2477412 a 0 + 7 chr8 8789343 8792004 a 0 + 8 chr12 4565015 4572004 a 0 - 9 chr17 4606158 4613079 a 0 + 10 chr21 5649868 5657579 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp_44xft6b/f1.bed -b /tmp/tmp_44xft6b/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr3 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp4n2rc7px/f1.bed -b /tmp/tmp4n2rc7px/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 5591744 5595931 a 0 - 1 chr1 5603572 5606999 a 0 - 2 chr11 9656467 9660252 a 0 - 3 chr17 3207892 3212079 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpmlpicc58/f1.bed -b /tmp/tmpmlpicc58/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpqrg5gxdu/f1.bed -b /tmp/tmpqrg5gxdu/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 9600744 9601196 a 0 - 1 chr15 7694914 7695366 a 0 - 2 chr17 7417479 7417931 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpyzvgy6os/f1.bed -b /tmp/tmpyzvgy6os/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp_ruyf7xs/f1.bed -b /tmp/tmp_ruyf7xs/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 7469852 7471972 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpdbt57g_g/f1.bed -b /tmp/tmpdbt57g_g/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmps4y0jwb2/f1.bed -b /tmp/tmps4y0jwb2/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 5465691 5466878 a 0 + 1 chr1 1017297 1017479 a 0 + 2 chr1 4916891 4919847 a 0 + 3 chr1 2359191 2361275 a 0 - 4 chr7 4916891 4918491 a 0 - 5 chr9 575754 577507 a 0 - 6 chr11 8868705 8872974 a 0 - 7 chr13 7195834 7204494 a 0 + 8 chr22 4940743 4948422 a 0 - 9 chrM 7974447 7982419 a 0 + 10 chrX 4916891 4924570 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpujuf7ux3/f1.bed -b /tmp/tmpujuf7ux3/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpn7iy4isk/f1.bed -b /tmp/tmpn7iy4isk/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 9170663 9171197 a 0 - 1 chr14 8325238 8325240 a 0 + 2 chr15 1265146 1267745 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp_uk8vgko/f1.bed -b /tmp/tmp_uk8vgko/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpo94kpsih/f1.bed -b /tmp/tmpo94kpsih/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1797135 1804187 a 0 - 1 chrM 6117669 6126460 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpxbhu5zao/f1.bed -b /tmp/tmpxbhu5zao/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmplkp_od_9/f1.bed -b /tmp/tmplkp_od_9/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1186173 1194085 a 0 + 1 chr1 7314536 7319979 a 0 + 2 chr1 7025106 7031644 a 0 + 3 chr1 101055 101183 a 0 + 4 chr1 1908775 1911751 a 0 - 5 chr1 9722689 9724716 a 0 - 6 chr3 5235194 5238170 a 0 + 7 chr4 68394 78190 a 0 + 8 chr17 9085956 9087401 a 0 + 9 chr17 1389589 1390834 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpc0ihvsgc/f1.bed -b /tmp/tmpc0ihvsgc/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpcywtt5bk/f1.bed -b /tmp/tmpcywtt5bk/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 9182832 9185370 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpfbtegf7n/f1.bed -b /tmp/tmpfbtegf7n/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpzc8t07ce/f1.bed -b /tmp/tmpzc8t07ce/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 9194542 9194956 a 0 + 1 chr1 4303576 4306379 a 0 + 2 chr1 7442432 7444878 a 0 + 3 chr1 7684538 7687796 a 0 - 4 chr1 8306882 8308324 a 0 - 5 chr2 9499 12757 a 0 - 6 chr13 9640154 9648821 a 0 - 7 chr14 1349647 1352450 a 0 + 8 chr16 4572669 4577508 a 0 + 9 chr18 3740233 3745325 a 0 - 10 chrM 5022585 5022586 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpnntuhgan/f1.bed -b /tmp/tmpnntuhgan/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpoa_n8qag/f1.bed -b /tmp/tmpoa_n8qag/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 87718 91289 a 0 + 1 chr1 2690515 2698196 a 0 + 2 chr1 6350270 6357452 a 0 - 3 chr1 2282126 2287038 a 0 - 4 chr1 930964 937745 a 0 - 5 chr1 2421919 2428402 a 0 - 6 chr1 4241903 4246681 a 0 - 7 chr1 5679711 5683764 a 0 - 8 chr1 5516184 5524432 a 0 - 9 chr10 7335608 7343265 a 0 - 10 chr22 930964 931024 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp0hebgzvc/f1.bed -b /tmp/tmp0hebgzvc/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp3xm4yw3s/f1.bed -b /tmp/tmp3xm4yw3s/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 92304 100475 a 0 + 1 chr21 4034945 4044353 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp0839rzu0/f1.bed -b /tmp/tmp0839rzu0/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp_dcete42/f1.bed -b /tmp/tmp_dcete42/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 2410816 2420439 a 0 + 1 chr1 8181604 8191227 a 0 + 2 chr1 536970 546593 a 0 + 3 chr1 10000000 10009623 a 0 + 4 chr1 6818256 6818965 a 0 + 5 chr1 3548637 3558260 a 0 - 6 chr1 7571834 7581457 a 0 - 7 chr17 1025542 1035165 a 0 + 8 chr18 5871543 5881166 a 0 + 9 chr19 8810070 8819693 a 0 + 10 chrY 963365 971937 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpl8g1f80m/f1.bed -b /tmp/tmpl8g1f80m/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpmfdimz33/f1.bed -b /tmp/tmpmfdimz33/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 6121916 6124694 a 0 + 1 chr1 2099074 2101051 a 0 + 2 chr1 9140976 9141145 a 0 + 3 chr1 5775459 5780139 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpx8_zsccg/f1.bed -b /tmp/tmpx8_zsccg/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 8582269 8586590 a 0 + 1 chr1 3290938 3294479 a 0 + 2 chr7 1 7639 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpyz553i_0/f1.bed -b /tmp/tmpyz553i_0/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr2 3596077 3596300 a 0 + 1 chr16 3851992 3855049 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpy4bz0hit/f1.bed -b /tmp/tmpy4bz0hit/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 3874460 3876429 a 0 + 1 chr1 5606458 5608442 a 0 + 2 chr1 7905476 7914566 a 0 + 3 chr22 8176408 8182602 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpt8ouj9f4/f1.bed -b /tmp/tmpt8ouj9f4/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 3639931 3649931 a 0 + 1 chr1 743878 747966 a 0 - 2 chr1 239909 239987 a 0 - 3 chr1 4873672 4881593 a 0 - 4 chr1 2414605 2419891 a 0 - 5 chr4 7708034 7708759 a 0 + 6 chr4 2981721 2984056 a 0 - 7 chr4 7708034 7710158 a 0 - 8 chr4 1162661 1167039 a 0 - 9 chr20 9831020 9837617 a 0 - 10 chr22 8062186 8071786 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpe61mopg_/f1.bed -b /tmp/tmpe61mopg_/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 9160 a 0 + 1 chr1 1 1360 a 0 - 2 chr6 1 7489 a 0 + 3 chr18 1 7949 a 0 - 4 chrY 1 10000 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpddaagy8n/f1.bed -b /tmp/tmpddaagy8n/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr12 9558711 9568710 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpbj3yhjzd/f1.bed -b /tmp/tmpbj3yhjzd/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 6556933 6561233 a 0 - 1 chr1 9761418 9770760 a 0 - 2 chr16 1571554 1575727 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp92_91stb/f1.bed -b /tmp/tmp92_91stb/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chrY 4870692 4877884 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp1npsz423/f1.bed -b /tmp/tmp1npsz423/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 7573869 7578380 a 0 + 1 chr7 5163335 5171080 a 0 + 2 chr9 3172971 3182583 a 0 + 3 chr20 1589901 1595253 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmppq2rjeqo/f1.bed -b /tmp/tmppq2rjeqo/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 6549285 6558387 a 0 - 1 chr1 2100580 2105540 a 0 - 2 chr2 6681327 6685369 a 0 + 3 chr11 7232885 7241873 a 0 - 4 chr12 1 7165 a 0 - 5 chr21 4321418 4326925 a 0 - 6 chrX 5751860 5756640 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpfl9vr42l/f1.bed -b /tmp/tmpfl9vr42l/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chrM 3891073 3897599 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpcvqesh2s/f1.bed -b /tmp/tmpcvqesh2s/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr21 6329553 6331711 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpuhn3604r/f1.bed -b /tmp/tmpuhn3604r/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 4978963 4982514 a 0 - 1 chr1 5298460 5300327 a 0 - 2 chr7 4978963 4982514 a 0 + 3 chr7 3247877 3249816 a 0 + 4 chr7 8302343 8305894 a 0 + 5 chr7 4978963 4986174 a 0 + 6 chr7 7924414 7927124 a 0 - 7 chr7 1068916 1076283 a 0 - 8 chr7 8604637 8613964 a 0 - 9 chr7 4978963 4983155 a 0 - 10 chrY 8044318 8048827 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp0_swlue0/f1.bed -b /tmp/tmp0_swlue0/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 6426183 6430166 a 0 - 1 chr5 7387005 7391887 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpnhwzz7bv/f1.bed -b /tmp/tmpnhwzz7bv/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr4 9937571 9939565 a 0 - 1 chrM 2805682 2814189 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpzg_d29r6/f1.bed -b /tmp/tmpzg_d29r6/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 8492579 8495568 a 0 - 1 chr10 9685032 9689256 a 0 + 2 chr10 4173082 4177634 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpdbf76t9z/f1.bed -b /tmp/tmpdbf76t9z/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 914961 915370 a 0 + 1 chr1 914961 916806 a 0 - 2 chr1 914961 924722 a 0 - 3 chr1 914961 919508 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpj4efh3t2/f1.bed -b /tmp/tmpj4efh3t2/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 4897455 4905480 a 0 + 1 chr1 1188244 1192391 a 0 - 2 chr1 1188244 1193519 a 0 - 3 chr1 9071786 9076970 a 0 - 4 chr4 6102122 6104073 a 0 - 5 chr11 8802100 8805632 a 0 - 6 chrY 8409917 8413564 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpeoilxxli/f1.bed -b /tmp/tmpeoilxxli/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 8165972 8168547 a 0 + 1 chr1 1632927 1633762 a 0 + 2 chr1 8772744 8782744 a 0 - 3 chr9 2893095 2903095 a 0 + 4 chr20 4400716 4410716 a 0 + 5 chr21 9471522 9481522 a 0 + 6 chr22 1183096 1184118 a 0 + 7 chrY 5983274 5993274 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpxy13n3wp/f1.bed -b /tmp/tmpxy13n3wp/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 2548390 2554219 a 0 - 1 chr13 7985697 7987725 a 0 + 2 chr20 3024434 3030344 a 0 + 3 chr21 3111417 3114585 a 0 + 4 chr21 2317021 2323082 a 0 - 5 chrX 157223 158736 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpqd2krp6o/f1.bed -b /tmp/tmpqd2krp6o/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 98914 99803 a 0 + 1 chr1 9387220 9395236 a 0 + 2 chr1 4758627 4768116 a 0 + 3 chr1 4732038 4737736 a 0 - 4 chr4 9999999 10005697 a 0 - 5 chr4 4823908 4829606 a 0 - 6 chrY 9159959 9165657 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpd0f65nw3/f1.bed -b /tmp/tmpd0f65nw3/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 3802031 3809400 a 0 + 1 chr1 3802031 3811920 a 0 + 2 chr1 3802031 3807616 a 0 - 3 chr2 6505717 6512108 a 0 - 4 chr3 10000000 10004464 a 0 - 5 chr21 3740634 3750476 a 0 + 6 chr22 8727312 8728526 a 0 + 7 chrM 3802031 3807899 a 0 + 8 chrX 3802031 3811522 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpj9sbysgx/f1.bed -b /tmp/tmpj9sbysgx/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 6717160 6725512 a 0 + 1 chr1 5329687 5339687 a 0 + 2 chr1 7063863 7069089 a 0 + 3 chr1 6625576 6631934 a 0 - 4 chr1 4801747 4806617 a 0 - 5 chr12 4801747 4810971 a 0 - 6 chrM 4801747 4803112 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpt3kv3d5e/f1.bed -b /tmp/tmpt3kv3d5e/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 8221266 8223884 a 0 + 1 chr18 9075163 9075757 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp0o9yixrb/f1.bed -b /tmp/tmp0o9yixrb/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr19 326443 329134 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpe6a2uvu0/f1.bed -b /tmp/tmpe6a2uvu0/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 6068339 6070313 a 0 + 1 chr1 2934401 2936375 a 0 + 2 chr1 4126789 4128763 a 0 + 3 chr8 342814 344788 a 0 - 4 chr21 172244 174218 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp5j8v_kl3/f1.bed -b /tmp/tmp5j8v_kl3/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chrM 9712039 9721752 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpnq49wyct/f1.bed -b /tmp/tmpnq49wyct/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 4858706 4866213 a 0 + 1 chr1 4858706 4859441 a 0 - 2 chr1 4725939 4728288 a 0 - 3 chr1 9426973 9436972 a 0 - 4 chr1 4858706 4864949 a 0 - 5 chr1 52480 58355 a 0 - 6 chr6 7864716 7869320 a 0 + 7 chr6 4858706 4865596 a 0 + 8 chr8 4858706 4866705 a 0 - 9 chr14 3024799 3028583 a 0 - 10 chr15 1971344 1974749 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp1ku8w7up/f1.bed -b /tmp/tmp1ku8w7up/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 4857300 4864352 a 0 + 1 chr10 6982883 6989935 a 0 + 2 chr13 1462095 1469147 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp9w5xrvhv/f1.bed -b /tmp/tmp9w5xrvhv/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 7784854 7785778 a 0 + 1 chr1 4807008 4812500 a 0 + 2 chr1 1148510 1158427 a 0 + 3 chr1 7815777 7818849 a 0 + 4 chr1 7717168 7723503 a 0 + 5 chr1 4445023 4449574 a 0 - 6 chr1 8703424 8708962 a 0 - 7 chr6 3646707 3647550 a 0 - 8 chr10 6557015 6558527 a 0 + 9 chr17 8423119 8424596 a 0 + 10 chr22 1769263 1775265 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpkzriijsu/f1.bed -b /tmp/tmpkzriijsu/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 3978293 3985395 a 0 - 1 chr1 3978293 3988293 a 0 - 2 chr1 3978293 3986998 a 0 - 3 chr1 3978293 3988293 a 0 - 4 chr1 3978293 3983235 a 0 - 5 chr1 7395786 7395996 a 0 - 6 chr1 8172727 8173715 a 0 - 7 chr5 2138074 2141759 a 0 + 8 chr8 3978293 3985277 a 0 - 9 chr15 3978293 3984453 a 0 - 10 chr17 3978293 3983688 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpndogvs3n/f1.bed -b /tmp/tmpndogvs3n/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1322968 1330433 a 0 + 1 chr1 1322968 1324586 a 0 + 2 chr1 9762655 9769796 a 0 - 3 chr1 1322968 1323002 a 0 - 4 chr2 1322968 1326386 a 0 + 5 chr2 8070904 8076982 a 0 - 6 chr7 1322968 1329815 a 0 - 7 chr11 1322968 1329260 a 0 + 8 chr11 1322968 1328053 a 0 - 9 chr11 5748336 5748722 a 0 - 10 chr14 1322968 1329880 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpka0gdo_4/f1.bed -b /tmp/tmpka0gdo_4/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr22 4737606 4745765 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpyhvvb58r/f1.bed -b /tmp/tmpyhvvb58r/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1416687 1416688 a 0 + 1 chr1 7930485 7931136 a 0 + 2 chr1 1416687 1424865 a 0 + 3 chr1 7492464 7497015 a 0 + 4 chr1 1416687 1417342 a 0 + 5 chr1 2022760 2023296 a 0 - 6 chr4 2901491 2908961 a 0 + 7 chr6 4799358 4806903 a 0 + 8 chr6 9937446 9947052 a 0 + 9 chr22 1416687 1420733 a 0 + 10 chr22 5812732 5813290 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpwucfhq2c/f1.bed -b /tmp/tmpwucfhq2c/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1028735 1030657 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp0svehs1t/f1.bed -b /tmp/tmp0svehs1t/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 8347010 8351703 a 0 + 1 chr1 3848294 3852612 a 0 + 2 chr1 429511 434013 a 0 + 3 chr1 6045881 6045888 a 0 - 4 chr1 2496895 2503968 a 0 - 5 chr1 4967770 4974784 a 0 - 6 chr18 107145 107686 a 0 + 7 chrX 3188766 3195788 a 0 + 8 chrX 1510051 1519858 a 0 + 9 chrX 1617968 1618998 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpksugymh_/f1.bed -b /tmp/tmpksugymh_/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 2497927 2507927 a 0 + 1 chr6 2350642 2359128 a 0 - 2 chr16 4715603 4724457 a 0 - 3 chr20 4675803 4684196 a 0 - 4 chr21 5068077 5076962 a 0 + 5 chrX 8148177 8151771 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpxx80cbp9/f1.bed -b /tmp/tmpxx80cbp9/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 5183221 5186247 a 0 + 1 chr1 5183221 5186718 a 0 + 2 chr1 5183221 5193221 a 0 + 3 chr1 5183221 5184007 a 0 + 4 chr1 5183221 5189524 a 0 + 5 chr3 4392526 4397982 a 0 + 6 chr8 5183221 5184841 a 0 + 7 chr12 5183221 5188330 a 0 + 8 chr15 5183221 5188022 a 0 + 9 chr21 5183221 5185865 a 0 + 10 chr21 7213984 7221300 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpw4skrt4i/f1.bed -b /tmp/tmpw4skrt4i/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1616397 1620447 a 0 + 1 chr1 9503905 9513852 a 0 - 2 chr1 8453748 8459919 a 0 - 3 chr12 2338272 2341126 a 0 + 4 chrY 1 8501 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp2eegudo0/f1.bed -b /tmp/tmp2eegudo0/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 4425908 4435786 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmplsjb3u8z/f1.bed -b /tmp/tmplsjb3u8z/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 8553434 8563363 a 0 - 1 chr1 251931 254781 a 0 - 2 chr1 4785629 4793670 a 0 - 3 chr1 181630 191630 a 0 - 4 chr3 2095636 2104350 a 0 - 5 chr3 6209074 6211924 a 0 - 6 chr3 8275360 8276950 a 0 - 7 chr3 6768430 6774836 a 0 - 8 chr16 8280545 8287162 a 0 - 9 chr18 43244 50819 a 0 - 10 chr18 1912770 1916338 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpmk1c53i7/f1.bed -b /tmp/tmpmk1c53i7/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 5647315 5655112 a 0 + 1 chr1 5717555 5726135 a 0 + 2 chr1 4492462 4494435 a 0 - 3 chr1 4393546 4395654 a 0 - 4 chr3 7012580 7015610 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpm5fdzlm6/f1.bed -b /tmp/tmpm5fdzlm6/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 4453780 4454137 a 0 + 1 chr1 3162609 3164988 a 0 + 2 chr1 8281402 8284711 a 0 + 3 chr1 8777265 8786029 a 0 + 4 chr1 3643155 3649930 a 0 + 5 chr1 1519268 1527067 a 0 + 6 chr1 4163838 4173297 a 0 - 7 chr16 3499045 3506986 a 0 + 8 chr17 5641802 5642056 a 0 + 9 chr19 2 10002 a 0 + 10 chr21 9664335 9668952 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp108v1_ov/f1.bed -b /tmp/tmp108v1_ov/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 8634817 8644461 a 0 + 1 chr1 7858769 7866913 a 0 - 2 chr1 8787788 8793636 a 0 - 3 chr1 4934408 4937576 a 0 - 4 chr1 2 6546 a 0 - 5 chr3 736274 739365 a 0 - 6 chr8 9885169 9888337 a 0 + 7 chr21 1751752 1751753 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpt8lhjvgq/f1.bed -b /tmp/tmpt8lhjvgq/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1223539 1226313 a 0 - 1 chr1 8280839 8283492 a 0 - 2 chr1 3910576 3919146 a 0 - 3 chr1 9030774 9039495 a 0 - 4 chr3 1944144 1946016 a 0 - 5 chr9 9999999 10002715 a 0 - 6 chr10 10000000 10002574 a 0 + 7 chr11 4314683 4323253 a 0 - 8 chr11 1711330 1719188 a 0 - 9 chrX 7092188 7100758 a 0 + 10 chrY 2107531 2115310 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp7zxn2ban/f1.bed -b /tmp/tmp7zxn2ban/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1151204 1156292 a 0 - 1 chr1 9721059 9727699 a 0 - 2 chr11 6460263 6464243 a 0 + 3 chr11 1903714 1905665 a 0 + 4 chr11 2326435 2330830 a 0 + 5 chr11 1 7177 a 0 + 6 chr11 5225205 5230293 a 0 + 7 chr11 1903714 1908802 a 0 - 8 chr11 1903714 1908802 a 0 - 9 chr11 5164868 5169956 a 0 - 10 chr11 1903714 1908802 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmprjdcfo8g/f1.bed -b /tmp/tmprjdcfo8g/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 8989332 8995780 a 0 - 1 chr3 8989332 8992810 a 0 + 2 chr15 8989332 8998127 a 0 + 3 chr16 8989332 8995322 a 0 - 4 chrY 8989332 8995987 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpavps0wtt/f1.bed -b /tmp/tmpavps0wtt/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 4503146 4504759 a 0 - 1 chr16 9779319 9788241 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp39d51f1d/f1.bed -b /tmp/tmp39d51f1d/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 6672813 6672814 a 0 + 1 chr1 3221580 3225155 a 0 + 2 chr1 8354658 8354659 a 0 + 3 chr15 2895883 2904805 a 0 + 4 chr22 3789536 3789537 a 0 + 5 chr22 9054391 9054392 a 0 + 6 chr22 8700971 8700972 a 0 - 7 chr22 239666 246594 a 0 - 8 chr22 4892066 4892067 a 0 - 9 chr22 7043247 7047071 a 0 - 10 chrY 9288194 9294519 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmps7kc8ssp/f1.bed -b /tmp/tmps7kc8ssp/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 9919621 9922937 a 0 - 1 chr1 1389566 1397291 a 0 - 2 chr1 6255814 6265243 a 0 - 3 chr6 9942221 9942803 a 0 - 4 chr6 7894644 7902304 a 0 - 5 chr16 4353580 4362605 a 0 - 6 chrY 7733183 7741482 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpxwd6zd07/f1.bed -b /tmp/tmpxwd6zd07/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 8336836 8340111 a 0 + 1 chr1 7002998 7012998 a 0 + 2 chr1 8219463 8223569 a 0 - 3 chr1 2236780 2237234 a 0 - 4 chr1 3995237 3999431 a 0 - 5 chr1 4337415 4338800 a 0 - 6 chr1 6957022 6960258 a 0 - 7 chr18 2971064 2974056 a 0 - 8 chr19 6583627 6583847 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpv_3hboam/f1.bed -b /tmp/tmpv_3hboam/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 4314240 4315424 a 0 - 1 chr1 1973674 1979615 a 0 - 2 chr1 3178456 3182319 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp2bzx0bz4/f1.bed -b /tmp/tmp2bzx0bz4/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr13 2493520 2493521 a 0 - 1 chr13 2493520 2494552 a 0 - 2 chrY 2493520 2494244 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpyu8_rv6z/f1.bed -b /tmp/tmpyu8_rv6z/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 4998829 5002076 a 0 + 1 chr1 3250139 3254813 a 0 + 2 chr1 9251273 9255667 a 0 - 3 chr1 3381196 3385902 a 0 - 4 chr1 4504724 4505765 a 0 - 5 chr1 7569759 7576159 a 0 - 6 chr3 5173911 5179094 a 0 + 7 chr5 4063717 4064882 a 0 + 8 chr8 1148068 1154662 a 0 - 9 chr12 5050269 5058958 a 0 + 10 chr14 9008995 9018760 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpo1flyhh2/f1.bed -b /tmp/tmpo1flyhh2/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 676569 680319 a 0 + 1 chr1 2060116 2065965 a 0 + 2 chr1 7308398 7316184 a 0 + 3 chr1 6379271 6384198 a 0 - 4 chr1 3035002 3035313 a 0 - 5 chr1 1182339 1188390 a 0 - 6 chr1 359921 362095 a 0 - 7 chr1 2761562 2766910 a 0 - 8 chr7 9999999 10004442 a 0 + 9 chr9 9014895 9016886 a 0 - 10 chr13 2483728 2487541 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp2jlxmooo/f1.bed -b /tmp/tmp2jlxmooo/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 7166191 7174410 a 0 + 1 chr1 3194705 3196568 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp5etgjj4s/f1.bed -b /tmp/tmp5etgjj4s/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 10000000 10002973 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpou6w6wcr/f1.bed -b /tmp/tmpou6w6wcr/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 3561692 3565284 a 0 - 1 chr1 7056739 7063448 a 0 - 2 chr1 6696965 6706574 a 0 - 3 chr14 7001027 7008080 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp_lfyqpc6/f1.bed -b /tmp/tmp_lfyqpc6/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 7897862 7901663 a 0 + 1 chr1 7054883 7057635 a 0 + 2 chr1 7897862 7903606 a 0 + 3 chr1 7897862 7901663 a 0 - 4 chr1 2784755 2793371 a 0 - 5 chr1 7897862 7901663 a 0 - 6 chr1 7897862 7905100 a 0 - 7 chr3 28774 32575 a 0 + 8 chr9 7897862 7901663 a 0 + 9 chr10 1742444 1743278 a 0 - 10 chr17 7897862 7902559 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpjgl1l0uh/f1.bed -b /tmp/tmpjgl1l0uh/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 7774072 7776181 a 0 + 1 chr1 6952857 6954027 a 0 + 2 chr1 4976388 4980942 a 0 + 3 chr2 8291593 8300867 a 0 + 4 chr18 2835118 2839863 a 0 + 5 chr18 5689966 5698580 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpgjwh0r1s/f1.bed -b /tmp/tmpgjwh0r1s/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 7998512 8007025 a 0 + 1 chr1 765917 774548 a 0 + 2 chr1 2428809 2434690 a 0 - 3 chr1 5257862 5259867 a 0 - 4 chr3 7329145 7339011 a 0 + 5 chr5 9848093 9849946 a 0 + 6 chr13 9814343 9820035 a 0 + 7 chr15 1133603 1143337 a 0 + 8 chr17 5990566 5999533 a 0 - 9 chr21 5241726 5244759 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpxhx7gqef/f1.bed -b /tmp/tmpxhx7gqef/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 6736839 6743920 a 0 + 1 chr1 9300538 9309868 a 0 - 2 chr5 3621443 3628914 a 0 + 3 chr5 7840336 7850317 a 0 + 4 chr5 4385783 4391700 a 0 + 5 chr5 4067619 4070646 a 0 + 6 chr5 9883764 9891875 a 0 + 7 chr5 4241431 4242520 a 0 + 8 chr5 4403359 4405047 a 0 - 9 chr5 5147754 5148355 a 0 - 10 chrM 8099703 8102824 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmplbs5zxji/f1.bed -b /tmp/tmplbs5zxji/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 707583 713377 a 0 + 1 chr4 707583 712928 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpawcsp8og/f1.bed -b /tmp/tmpawcsp8og/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1428973 1438887 a 0 + 1 chr1 4715745 4723145 a 0 + 2 chr1 3614530 3622107 a 0 + 3 chr1 6596315 6596802 a 0 + 4 chr1 8724779 8734693 a 0 - 5 chr3 820457 830371 a 0 + 6 chr5 238366 239445 a 0 + 7 chr11 43491 53405 a 0 + 8 chr17 8872636 8882550 a 0 + 9 chr21 2019489 2029403 a 0 - 10 chr21 8633136 8643050 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpdv4qs7a3/f1.bed -b /tmp/tmpdv4qs7a3/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 7070705 7078906 a 0 + 1 chr1 7070705 7078823 a 0 + 2 chr1 7070705 7079373 a 0 + 3 chr1 7070705 7073946 a 0 + 4 chr1 7070705 7074629 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmplkeqn1fi/f1.bed -b /tmp/tmplkeqn1fi/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 6078495 6079361 a 0 + 1 chr1 9411024 9413899 a 0 - 2 chr12 5683862 5688291 a 0 - 3 chrY 9123718 9131083 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpv9966w59/f1.bed -b /tmp/tmpv9966w59/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 8748782 8753588 a 0 - 1 chr1 6950610 6953492 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpjey9572i/f1.bed -b /tmp/tmpjey9572i/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 10000000 10002814 a 0 + 1 chr1 1574664 1581645 a 0 - 2 chr13 5616885 5619820 a 0 - 3 chr14 9028807 9033865 a 0 - 4 chr21 5572720 5578622 a 0 + 5 chr22 9477219 9477430 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp9bg43vct/f1.bed -b /tmp/tmp9bg43vct/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1685920 1687121 a 0 + 1 chr1 4807424 4807426 a 0 + 2 chr1 9424045 9431483 a 0 + 3 chr1 2442601 2449217 a 0 + 4 chr1 3251832 3252310 a 0 - 5 chr1 8023312 8025137 a 0 - 6 chr1 8153502 8156896 a 0 - 7 chr3 8276407 8282192 a 0 - 8 chr14 2345729 2354771 a 0 + 9 chr14 556733 561465 a 0 + 10 chrM 5444626 5452797 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp2dwikuko/f1.bed -b /tmp/tmp2dwikuko/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 3498605 3504813 a 0 + 1 chr1 8817626 8823754 a 0 + 2 chr1 6238996 6247902 a 0 + 3 chr1 7012521 7020237 a 0 - 4 chr1 6163011 6168003 a 0 - 5 chr1 10000000 10007193 a 0 - 6 chr8 4663384 4665998 a 0 - 7 chr11 8742373 8748074 a 0 + 8 chr11 5415865 5423058 a 0 - 9 chr16 2 1170 a 0 - 10 chr18 4138637 4143307 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpub74ngjk/f1.bed -b /tmp/tmpub74ngjk/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 7995561 7999710 a 0 + 1 chr1 1741037 1741647 a 0 + 2 chr1 5414216 5414826 a 0 - 3 chr1 4815958 4818564 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpfq7l8li5/f1.bed -b /tmp/tmpfq7l8li5/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr12 3824405 3830469 a 0 - 1 chr17 6205984 6214183 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpdfk4ql1f/f1.bed -b /tmp/tmpdfk4ql1f/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 7029767 7038692 a 0 + 1 chr1 8170423 8176927 a 0 + 2 chr1 6861771 6865431 a 0 - 3 chr2 8170423 8180135 a 0 - 4 chr18 3351636 3360267 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpm5eftk3y/f1.bed -b /tmp/tmpm5eftk3y/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 5853908 5856499 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmplh5jac2k/f1.bed -b /tmp/tmplh5jac2k/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 6808705 6811726 a 0 + 1 chr1 2875065 2877854 a 0 + 2 chr1 4318917 4325032 a 0 + 3 chr1 9202997 9205489 a 0 - 4 chr1 7399321 7402342 a 0 - 5 chr1 8097073 8100094 a 0 - 6 chr1 4189879 4192900 a 0 - 7 chr1 1636406 1644273 a 0 - 8 chr1 7842413 7848486 a 0 - 9 chr1 2851651 2856851 a 0 - 10 chr1 6907667 6909664 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmphk71gpnf/f1.bed -b /tmp/tmphk71gpnf/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr17 2045302 2053354 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpzyof_x70/f1.bed -b /tmp/tmpzyof_x70/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1031673 1036944 a 0 + 1 chr1 8173260 8178531 a 0 + 2 chr1 8218360 8223631 a 0 + 3 chr1 1165408 1170679 a 0 + 4 chr1 5412264 5421245 a 0 - 5 chr1 2445906 2451177 a 0 - 6 chr1 5312513 5317784 a 0 - 7 chr1 897886 903157 a 0 - 8 chr1 9332836 9338107 a 0 - 9 chr1 79501 83573 a 0 - 10 chr13 465799 469996 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpxgcf_1fx/f1.bed -b /tmp/tmpxgcf_1fx/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 10000000 10000602 a 0 + 1 chr1 7612988 7613206 a 0 + 2 chr1 6530907 6533373 a 0 + 3 chr1 7959583 7964477 a 0 - 4 chr1 7523308 7524011 a 0 - 5 chr1 9504975 9512183 a 0 - 6 chr1 3806274 3815159 a 0 - 7 chr2 4991226 5001226 a 0 - 8 chr11 845241 853743 a 0 + 9 chr11 9315964 9325734 a 0 - 10 chr11 8877185 8877186 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp8jcw8co5/f1.bed -b /tmp/tmp8jcw8co5/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 9119732 9122530 a 0 + 1 chr1 5264231 5267881 a 0 - 2 chr1 4661122 4663038 a 0 - 3 chr11 9119732 9119935 a 0 + 4 chr16 2323450 2332356 a 0 + 5 chr17 1154877 1156842 a 0 + 6 chr19 5424531 5430498 a 0 - 7 chr21 9119732 9127213 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpy0pq5uqx/f1.bed -b /tmp/tmpy0pq5uqx/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 9292667 9300905 a 0 + 1 chr11 817519 827225 a 0 - 2 chr13 1389209 1398415 a 0 + 3 chr17 8813778 8820902 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp1kq4yxyc/f1.bed -b /tmp/tmp1kq4yxyc/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 4333316 4337589 a 0 + 1 chr1 6321127 6325400 a 0 + 2 chr1 2871670 2874668 a 0 - 3 chr7 6881927 6886200 a 0 + 4 chr11 2421754 2426027 a 0 + 5 chr20 9873937 9878210 a 0 + 6 chr20 7135435 7139708 a 0 + 7 chr20 2196119 2200392 a 0 + 8 chr20 6812183 6816456 a 0 + 9 chr20 9997755 10004901 a 0 - 10 chr20 4063728 4068001 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpxus9nldy/f1.bed -b /tmp/tmpxus9nldy/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 6649948 6650302 a 0 + 1 chr1 3288927 3295819 a 0 + 2 chr7 6966201 6975963 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpblyj0c23/f1.bed -b /tmp/tmpblyj0c23/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 725935 729515 a 0 - 1 chr1 3410567 3420563 a 0 - 2 chr1 2 7666 a 0 - 3 chr7 804911 808300 a 0 + 4 chr15 2 8656 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp95jxm3cg/f1.bed -b /tmp/tmp95jxm3cg/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr4 2629991 2634718 a 0 + 1 chr20 5231022 5235749 a 0 + 2 chr20 897494 902221 a 0 + 3 chr20 6062234 6066961 a 0 + 4 chr20 435565 440292 a 0 + 5 chr20 8242530 8247257 a 0 + 6 chr20 3266965 3271692 a 0 - 7 chr20 7235394 7240121 a 0 - 8 chr20 3422285 3427012 a 0 - 9 chr20 4597007 4598316 a 0 - 10 chr20 1 6084 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp__89itth/f1.bed -b /tmp/tmp__89itth/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 6651951 6661300 a 0 + 1 chr1 1262364 1271713 a 0 + 2 chr1 6651951 6654028 a 0 + 3 chr1 3755778 3765127 a 0 + 4 chr1 6651951 6661300 a 0 - 5 chr1 6651951 6661300 a 0 - 6 chr1 6651951 6661300 a 0 - 7 chr7 6651951 6661181 a 0 - 8 chr10 10000000 10009349 a 0 + 9 chr11 1071919 1081268 a 0 - 10 chr21 6651951 6661300 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmppyju2gcy/f1.bed -b /tmp/tmppyju2gcy/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 6376390 6379176 a 0 + 1 chr1 6731824 6735620 a 0 - 2 chr1 3007530 3014929 a 0 - 3 chr1 3418975 3422771 a 0 - 4 chr5 2706168 2709964 a 0 - 5 chr6 5474122 5477918 a 0 + 6 chr19 9907171 9913262 a 0 - 7 chr20 9636941 9637902 a 0 - 8 chr22 9341952 9343535 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp5nkzlrh5/f1.bed -b /tmp/tmp5nkzlrh5/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 5196551 5198749 a 0 + 1 chr1 1046594 1054679 a 0 - 2 chr1 3070306 3070385 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpa9f52k1v/f1.bed -b /tmp/tmpa9f52k1v/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 5223971 5231992 a 0 + 1 chr1 8471018 8477580 a 0 + 2 chr1 2614340 2616951 a 0 + 3 chr1 6927860 6932319 a 0 - 4 chr1 3358143 3361798 a 0 - 5 chr1 9706293 9709255 a 0 - 6 chr1 3894482 3903227 a 0 - 7 chr12 1242873 1245685 a 0 - 8 chr16 7210375 7214452 a 0 - 9 chr19 605184 613465 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpgdxptarz/f1.bed -b /tmp/tmpgdxptarz/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr15 6859376 6869376 a 0 + 1 chr21 7794720 7804719 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpcpi9l2ow/f1.bed -b /tmp/tmpcpi9l2ow/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 4189117 4192096 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp9i0f5lgz/f1.bed -b /tmp/tmp9i0f5lgz/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 5283221 5293221 a 0 + 1 chr1 4785697 4788068 a 0 + 2 chr1 5089962 5099962 a 0 - 3 chr1 5089962 5099962 a 0 - 4 chr1 3775059 3785059 a 0 - 5 chr1 6781850 6791850 a 0 - 6 chr7 8361415 8371415 a 0 + 7 chr13 5788898 5790033 a 0 - 8 chr20 4269403 4279403 a 0 - 9 chrY 5089962 5099962 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp7072z767/f1.bed -b /tmp/tmp7072z767/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 4717727 4719922 a 0 + 1 chr1 7632136 7642136 a 0 - 2 chr1 3268122 3271396 a 0 - 3 chr8 964311 964648 a 0 + 4 chr18 5726969 5728681 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp1_shb6vx/f1.bed -b /tmp/tmp1_shb6vx/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 7493985 7499070 a 0 - 1 chr5 4724709 4727602 a 0 - 2 chr14 5440793 5446966 a 0 - 3 chrX 8052567 8058740 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpbdy72gl7/f1.bed -b /tmp/tmpbdy72gl7/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 3618031 3619897 a 0 + 1 chr1 361054 363685 a 0 + 2 chr1 9632831 9642307 a 0 + 3 chr1 558157 560184 a 0 - 4 chr1 10000000 10004079 a 0 - 5 chr2 1223026 1231101 a 0 + 6 chr6 764978 773797 a 0 - 7 chr18 4417579 4425469 a 0 + 8 chr22 2811722 2814795 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpzhnzxoki/f1.bed -b /tmp/tmpzhnzxoki/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 5404831 5411543 a 0 + 1 chr1 5404831 5412762 a 0 - 2 chr1 9787628 9794807 a 0 - 3 chr1 7551761 7554364 a 0 - 4 chr1 5289647 5293243 a 0 - 5 chr1 5404831 5408644 a 0 - 6 chr2 476680 485899 a 0 - 7 chr4 6311324 6319222 a 0 + 8 chr6 5404831 5413065 a 0 - 9 chr9 5404831 5407455 a 0 + 10 chr15 5404831 5405386 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp28jy59_5/f1.bed -b /tmp/tmp28jy59_5/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr9 5179424 5179548 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpaq9zh_hv/f1.bed -b /tmp/tmpaq9zh_hv/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1751928 1758967 a 0 - 1 chr1 4458897 4460997 a 0 - 2 chr1 8375620 8385619 a 0 - 3 chr4 7220591 7222691 a 0 + 4 chr16 9011503 9018862 a 0 + 5 chrM 1747723 1749359 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmppmlx775s/f1.bed -b /tmp/tmppmlx775s/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1071227 1072793 a 0 + 1 chr1 8405705 8410377 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp0ghim2dp/f1.bed -b /tmp/tmp0ghim2dp/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 6757109 6767014 a 0 + 1 chr1 8849232 8852576 a 0 - 2 chr2 1127413 1137318 a 0 - 3 chr3 7418896 7428280 a 0 - 4 chr6 7255511 7265416 a 0 - 5 chr13 9362619 9372524 a 0 + 6 chr14 9384394 9394320 a 0 - 7 chr15 9050762 9056979 a 0 + 8 chr18 9416415 9416416 a 0 + 9 chr20 9416415 9424895 a 0 + 10 chr20 1883683 1890268 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp_4dz0k_2/f1.bed -b /tmp/tmp_4dz0k_2/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 8553434 8563363 a 0 - 1 chr1 251931 254781 a 0 - 2 chr1 4785629 4793670 a 0 - 3 chr1 181630 191630 a 0 - 4 chr3 2095636 2104350 a 0 - 5 chr3 6209074 6211924 a 0 - 6 chr3 8275360 8276950 a 0 - 7 chr3 6768430 6774836 a 0 - 8 chr16 8280545 8287162 a 0 - 9 chr18 43244 50819 a 0 - 10 chr18 1912770 1916338 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmptjhakapu/f1.bed -b /tmp/tmptjhakapu/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr9 5179424 5179548 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpt2wr_lny/f1.bed -b /tmp/tmpt2wr_lny/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 10000000 10000602 a 0 + 1 chr1 7612988 7613206 a 0 + 2 chr1 6530907 6533373 a 0 + 3 chr1 7959583 7964477 a 0 - 4 chr1 7523308 7524011 a 0 - 5 chr1 9504975 9512183 a 0 - 6 chr1 3806274 3815159 a 0 - 7 chr2 4991226 5001226 a 0 - 8 chr11 845241 853743 a 0 + 9 chr11 9315964 9325734 a 0 - 10 chr11 8877185 8877186 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpnqotxhgy/f1.bed -b /tmp/tmpnqotxhgy/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 8347010 8351703 a 0 + 1 chr1 3848294 3852612 a 0 + 2 chr1 429511 434013 a 0 + 3 chr1 6045881 6045888 a 0 - 4 chr1 2496895 2503968 a 0 - 5 chr1 4967770 4974784 a 0 - 6 chr18 107145 107686 a 0 + 7 chrX 3188766 3195788 a 0 + 8 chrX 1510051 1519858 a 0 + 9 chrX 1617968 1618998 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpldiik0lk/f1.bed -b /tmp/tmpldiik0lk/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 6549285 6558387 a 0 - 1 chr1 2100580 2105540 a 0 - 2 chr2 6681327 6685369 a 0 + 3 chr11 7232885 7241873 a 0 - 4 chr12 1 7165 a 0 - 5 chr21 4321418 4326925 a 0 - 6 chrX 5751860 5756640 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpe5k6kvaw/f1.bed -b /tmp/tmpe5k6kvaw/f2.bed Chromosome Start End Name Score Strand 0 chr1 9202640 9202641 a 0 + Chromosome Start End Name Score Strand 0 chr1 3498605 3504813 a 0 + 1 chr1 8817626 8823754 a 0 + 2 chr1 6238996 6247902 a 0 + 3 chr1 7012521 7020237 a 0 - 4 chr1 6163011 6168003 a 0 - 5 chr1 10000000 10007193 a 0 - 6 chr8 4663384 4665998 a 0 - 7 chr11 8742373 8748074 a 0 + 8 chr11 5415865 5423058 a 0 - 9 chr16 2 1170 a 0 - 10 chr18 4138637 4143307 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpezn6ijgm/f1.bed -b /tmp/tmpezn6ijgm/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1416687 1416688 a 0 + 1 chr1 7930485 7931136 a 0 + 2 chr1 1416687 1424865 a 0 + 3 chr1 7492464 7497015 a 0 + 4 chr1 1416687 1417342 a 0 + 5 chr1 2022760 2023296 a 0 - 6 chr4 2901491 2908961 a 0 + 7 chr6 4799358 4806903 a 0 + 8 chr6 9937446 9947052 a 0 + 9 chr22 1416687 1420733 a 0 + 10 chr22 5812732 5813290 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpw0in5ufl/f1.bed -b /tmp/tmpw0in5ufl/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 7166191 7174410 a 0 + 1 chr1 3194705 3196568 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpqo2cj8ai/f1.bed -b /tmp/tmpqo2cj8ai/f2.bed Chromosome Start End Name Score Strand 0 chr16 5584984 5584985 a 0 + Chromosome Start End Name Score Strand 0 chr1 8582269 8586590 a 0 + 1 chr1 3290938 3294479 a 0 + 2 chr7 1 7639 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp9o7nfevp/f1.bed -b /tmp/tmp9o7nfevp/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 10000000 10002973 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpi_gbi6v6/f1.bed -b /tmp/tmpi_gbi6v6/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr6 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 6078495 6079361 a 0 + 1 chr1 9411024 9413899 a 0 - 2 chr12 5683862 5688291 a 0 - 3 chrY 9123718 9131083 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpo6t5u4pr/f1.bed -b /tmp/tmpo6t5u4pr/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 8582269 8586590 a 0 + 1 chr1 3290938 3294479 a 0 + 2 chr7 1 7639 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpmrbzxssw/f1.bed -b /tmp/tmpmrbzxssw/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 8221266 8223884 a 0 + 1 chr18 9075163 9075757 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpffq613z1/f1.bed -b /tmp/tmpffq613z1/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr13 2493520 2493521 a 0 - 1 chr13 2493520 2494552 a 0 - 2 chrY 2493520 2494244 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp95rkw87j/f1.bed -b /tmp/tmp95rkw87j/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr2 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 5223971 5231992 a 0 + 1 chr1 8471018 8477580 a 0 + 2 chr1 2614340 2616951 a 0 + 3 chr1 6927860 6932319 a 0 - 4 chr1 3358143 3361798 a 0 - 5 chr1 9706293 9709255 a 0 - 6 chr1 3894482 3903227 a 0 - 7 chr12 1242873 1245685 a 0 - 8 chr16 7210375 7214452 a 0 - 9 chr19 605184 613465 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp_ypd14sl/f1.bed -b /tmp/tmp_ypd14sl/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 4998829 5002076 a 0 + 1 chr1 3250139 3254813 a 0 + 2 chr1 9251273 9255667 a 0 - 3 chr1 3381196 3385902 a 0 - 4 chr1 4504724 4505765 a 0 - 5 chr1 7569759 7576159 a 0 - 6 chr3 5173911 5179094 a 0 + 7 chr5 4063717 4064882 a 0 + 8 chr8 1148068 1154662 a 0 - 9 chr12 5050269 5058958 a 0 + 10 chr14 9008995 9018760 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpvd47hv_3/f1.bed -b /tmp/tmpvd47hv_3/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 9160 a 0 + 1 chr1 1 1360 a 0 - 2 chr6 1 7489 a 0 + 3 chr18 1 7949 a 0 - 4 chrY 1 10000 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp9byy5a6k/f1.bed -b /tmp/tmp9byy5a6k/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 7897862 7901663 a 0 + 1 chr1 7054883 7057635 a 0 + 2 chr1 7897862 7903606 a 0 + 3 chr1 7897862 7901663 a 0 - 4 chr1 2784755 2793371 a 0 - 5 chr1 7897862 7901663 a 0 - 6 chr1 7897862 7905100 a 0 - 7 chr3 28774 32575 a 0 + 8 chr9 7897862 7901663 a 0 + 9 chr10 1742444 1743278 a 0 - 10 chr17 7897862 7902559 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp5oy43tok/f1.bed -b /tmp/tmp5oy43tok/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 3978293 3985395 a 0 - 1 chr1 3978293 3988293 a 0 - 2 chr1 3978293 3986998 a 0 - 3 chr1 3978293 3988293 a 0 - 4 chr1 3978293 3983235 a 0 - 5 chr1 7395786 7395996 a 0 - 6 chr1 8172727 8173715 a 0 - 7 chr5 2138074 2141759 a 0 + 8 chr8 3978293 3985277 a 0 - 9 chr15 3978293 3984453 a 0 - 10 chr17 3978293 3983688 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp5cjedbi2/f1.bed -b /tmp/tmp5cjedbi2/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 5647315 5655112 a 0 + 1 chr1 5717555 5726135 a 0 + 2 chr1 4492462 4494435 a 0 - 3 chr1 4393546 4395654 a 0 - 4 chr3 7012580 7015610 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpoo8l6hr9/f1.bed -b /tmp/tmpoo8l6hr9/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 10000000 10002814 a 0 + 1 chr1 1574664 1581645 a 0 - 2 chr13 5616885 5619820 a 0 - 3 chr14 9028807 9033865 a 0 - 4 chr21 5572720 5578622 a 0 + 5 chr22 9477219 9477430 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmphe90ohz0/f1.bed -b /tmp/tmphe90ohz0/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 8553434 8563363 a 0 - 1 chr1 251931 254781 a 0 - 2 chr1 4785629 4793670 a 0 - 3 chr1 181630 191630 a 0 - 4 chr3 2095636 2104350 a 0 - 5 chr3 6209074 6211924 a 0 - 6 chr3 8275360 8276950 a 0 - 7 chr3 6768430 6774836 a 0 - 8 chr16 8280545 8287162 a 0 - 9 chr18 43244 50819 a 0 - 10 chr18 1912770 1916338 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp4fiphowh/f1.bed -b /tmp/tmp4fiphowh/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 3618031 3619897 a 0 + 1 chr1 361054 363685 a 0 + 2 chr1 9632831 9642307 a 0 + 3 chr1 558157 560184 a 0 - 4 chr1 10000000 10004079 a 0 - 5 chr2 1223026 1231101 a 0 + 6 chr6 764978 773797 a 0 - 7 chr18 4417579 4425469 a 0 + 8 chr22 2811722 2814795 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpkq5u5ku8/f1.bed -b /tmp/tmpkq5u5ku8/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr21 6329553 6331711 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpe3doe2c_/f1.bed -b /tmp/tmpe3doe2c_/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1031673 1036944 a 0 + 1 chr1 8173260 8178531 a 0 + 2 chr1 8218360 8223631 a 0 + 3 chr1 1165408 1170679 a 0 + 4 chr1 5412264 5421245 a 0 - 5 chr1 2445906 2451177 a 0 - 6 chr1 5312513 5317784 a 0 - 7 chr1 897886 903157 a 0 - 8 chr1 9332836 9338107 a 0 - 9 chr1 79501 83573 a 0 - 10 chr13 465799 469996 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpk52yncmv/f1.bed -b /tmp/tmpk52yncmv/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 4857300 4864352 a 0 + 1 chr10 6982883 6989935 a 0 + 2 chr13 1462095 1469147 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmphqby7f33/f1.bed -b /tmp/tmphqby7f33/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 8553434 8563363 a 0 - 1 chr1 251931 254781 a 0 - 2 chr1 4785629 4793670 a 0 - 3 chr1 181630 191630 a 0 - 4 chr3 2095636 2104350 a 0 - 5 chr3 6209074 6211924 a 0 - 6 chr3 8275360 8276950 a 0 - 7 chr3 6768430 6774836 a 0 - 8 chr16 8280545 8287162 a 0 - 9 chr18 43244 50819 a 0 - 10 chr18 1912770 1916338 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpai67lpig/f1.bed -b /tmp/tmpai67lpig/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 6556933 6561233 a 0 - 1 chr1 9761418 9770760 a 0 - 2 chr16 1571554 1575727 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpqbv_ix9r/f1.bed -b /tmp/tmpqbv_ix9r/f2.bed Chromosome Start End Name Score Strand 0 chr11 1 2 a 0 + 1 chr11 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 10000000 10002973 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpcstk8zfd/f1.bed -b /tmp/tmpcstk8zfd/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 914961 915370 a 0 + 1 chr1 914961 916806 a 0 - 2 chr1 914961 924722 a 0 - 3 chr1 914961 919508 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmppnk44wtq/f1.bed -b /tmp/tmppnk44wtq/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1071227 1072793 a 0 + 1 chr1 8405705 8410377 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmppw7nzfj5/f1.bed -b /tmp/tmppw7nzfj5/f2.bed Chromosome Start End Name Score Strand 0 chr10 1041669 1041926 a 0 + Chromosome Start End Name Score Strand 0 chr1 5404831 5411543 a 0 + 1 chr1 5404831 5412762 a 0 - 2 chr1 9787628 9794807 a 0 - 3 chr1 7551761 7554364 a 0 - 4 chr1 5289647 5293243 a 0 - 5 chr1 5404831 5408644 a 0 - 6 chr2 476680 485899 a 0 - 7 chr4 6311324 6319222 a 0 + 8 chr6 5404831 5413065 a 0 - 9 chr9 5404831 5407455 a 0 + 10 chr15 5404831 5405386 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpfvn58rjr/f1.bed -b /tmp/tmpfvn58rjr/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 6757109 6767014 a 0 + 1 chr1 8849232 8852576 a 0 - 2 chr2 1127413 1137318 a 0 - 3 chr3 7418896 7428280 a 0 - 4 chr6 7255511 7265416 a 0 - 5 chr13 9362619 9372524 a 0 + 6 chr14 9384394 9394320 a 0 - 7 chr15 9050762 9056979 a 0 + 8 chr18 9416415 9416416 a 0 + 9 chr20 9416415 9424895 a 0 + 10 chr20 1883683 1890268 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp156ubme1/f1.bed -b /tmp/tmp156ubme1/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 7070705 7078906 a 0 + 1 chr1 7070705 7078823 a 0 + 2 chr1 7070705 7079373 a 0 + 3 chr1 7070705 7073946 a 0 + 4 chr1 7070705 7074629 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp7qitytqj/f1.bed -b /tmp/tmp7qitytqj/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + 4 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 4897455 4905480 a 0 + 1 chr1 1188244 1192391 a 0 - 2 chr1 1188244 1193519 a 0 - 3 chr1 9071786 9076970 a 0 - 4 chr4 6102122 6104073 a 0 - 5 chr11 8802100 8805632 a 0 - 6 chrY 8409917 8413564 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpu4yhkr16/f1.bed -b /tmp/tmpu4yhkr16/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 4978963 4982514 a 0 - 1 chr1 5298460 5300327 a 0 - 2 chr7 4978963 4982514 a 0 + 3 chr7 3247877 3249816 a 0 + 4 chr7 8302343 8305894 a 0 + 5 chr7 4978963 4986174 a 0 + 6 chr7 7924414 7927124 a 0 - 7 chr7 1068916 1076283 a 0 - 8 chr7 8604637 8613964 a 0 - 9 chr7 4978963 4983155 a 0 - 10 chrY 8044318 8048827 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpf2kqkpsu/f1.bed -b /tmp/tmpf2kqkpsu/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 5196551 5198749 a 0 + 1 chr1 1046594 1054679 a 0 - 2 chr1 3070306 3070385 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmprgutkj1r/f1.bed -b /tmp/tmprgutkj1r/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + 4 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 8165972 8168547 a 0 + 1 chr1 1632927 1633762 a 0 + 2 chr1 8772744 8782744 a 0 - 3 chr9 2893095 2903095 a 0 + 4 chr20 4400716 4410716 a 0 + 5 chr21 9471522 9481522 a 0 + 6 chr22 1183096 1184118 a 0 + 7 chrY 5983274 5993274 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpza3xdroy/f1.bed -b /tmp/tmpza3xdroy/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 9919621 9922937 a 0 - 1 chr1 1389566 1397291 a 0 - 2 chr1 6255814 6265243 a 0 - 3 chr6 9942221 9942803 a 0 - 4 chr6 7894644 7902304 a 0 - 5 chr16 4353580 4362605 a 0 - 6 chrY 7733183 7741482 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpeqrl_wjd/f1.bed -b /tmp/tmpeqrl_wjd/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 4425908 4435786 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp4ixiecfa/f1.bed -b /tmp/tmp4ixiecfa/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1751928 1758967 a 0 - 1 chr1 4458897 4460997 a 0 - 2 chr1 8375620 8385619 a 0 - 3 chr4 7220591 7222691 a 0 + 4 chr16 9011503 9018862 a 0 + 5 chrM 1747723 1749359 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp38mwoj3i/f1.bed -b /tmp/tmp38mwoj3i/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr2 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 6549285 6558387 a 0 - 1 chr1 2100580 2105540 a 0 - 2 chr2 6681327 6685369 a 0 + 3 chr11 7232885 7241873 a 0 - 4 chr12 1 7165 a 0 - 5 chr21 4321418 4326925 a 0 - 6 chrX 5751860 5756640 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp0o3cgyuw/f1.bed -b /tmp/tmp0o3cgyuw/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpuj4g8bfh/f1.bed -b /tmp/tmpuj4g8bfh/f2.bed ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ____________ test_three_in_a_row[strandedness_chain2-method_chain2] ____________ [gw5] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', False), method_chain = ('set_union', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('set_union', 'overlap'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E (and 182 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BUq3TeoKg2lZGRAQsAAD8PAnI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ___________________ test_k_nearest[upstream-True-False-last] ___________________ [gw4] linux -- Python 3.12.6 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 880, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 510, in test_k_nearest | @pytest.mark.explore | ^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1722, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 548, in test_k_nearest | result = gr.k_nearest( | ^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2450, in k_nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 292, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 180, in _nearest | df = __nearest(d1, d2, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 140, in nearest_next | lidx, ridx, dist = nearest_next_idx(d1, d2, d1.__k__.values, ties) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 56, in nearest_next_idx | lidx, ridx_pos, dist = k_nearest_next_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/k_nearest.pyx", line 55, in sorted_nearest.src.k_nearest.k_nearest_next_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_k_nearest( | nearest_how='upstream', | overlap=True, | strandedness=False, | ties='last', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:160 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:171 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:41 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:42 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:46 | (and 38 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2TAAIyMmGIMAAB5AAQ=') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 548, in test_k_nearest | result = gr.k_nearest( | ^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2450, in k_nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 292, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 180, in _nearest | df = __nearest(d1, d2, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 115, in nearest_previous | lidx, ridx, dist = nearest_previous_idx(d1, d2, d1.__k__.values, ties) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 28, in nearest_previous_idx | lidx, ridx_pos, dist = k_nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/k_nearest.pyx", line 28, in sorted_nearest.src.k_nearest.k_nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_k_nearest( | nearest_how='upstream', | overlap=True, | strandedness=False, | ties='last', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:14 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:15 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:160 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:171 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:19 | (and 37 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2TABIxYxAAAZAAD') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_vg6gbsj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_vg6gbsj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp10ii6f0l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp10ii6f0l/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpe1ob60s1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe1ob60s1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4tyucs9y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4tyucs9y/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp52wm0hsv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp52wm0hsv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmvgq6lp4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmvgq6lp4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2d0z9gif/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2d0z9gif/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpixnq7i00/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpixnq7i00/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpt9bw8m5e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt9bw8m5e/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpg4h7kiuk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg4h7kiuk/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpn4ycdbzj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn4ycdbzj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmjwxvb2j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmjwxvb2j/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmptre1en8f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptre1en8f/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyf93q_bk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyf93q_bk/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnu21egqj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnu21egqj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp95wvkgqu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp95wvkgqu/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpok0vi42e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpok0vi42e/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxw2qp_g0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxw2qp_g0/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmph8f6opq6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph8f6opq6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpt70ea5xq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt70ea5xq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmphhbyct61/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphhbyct61/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpe3_zuoln/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe3_zuoln/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp69culsxn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp69culsxn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpn4dl8zmr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn4dl8zmr/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmps89u5p4a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps89u5p4a/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmptdcvloar/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptdcvloar/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjk8_mu7s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjk8_mu7s/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpm86z3t9n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm86z3t9n/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9topwcp8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9topwcp8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmplovxlqrk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplovxlqrk/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp89hiv0eb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp89hiv0eb/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpm9ppp2jt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm9ppp2jt/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgv7fpls1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgv7fpls1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmptk1x_sg_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptk1x_sg_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmprdk9fg8w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprdk9fg8w/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpja79tzf3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpja79tzf3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwg5yfu3i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwg5yfu3i/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_2agb6ie/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_2agb6ie/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdsj8xrwk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdsj8xrwk/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpd_gl7803/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd_gl7803/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpc8cglpog/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc8cglpog/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmphvkz2ejf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphvkz2ejf/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3v1jy5tu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3v1jy5tu/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjfsnpnhz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjfsnpnhz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpv23pycfa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv23pycfa/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp65_qwz0w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp65_qwz0w/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxx576w9c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxx576w9c/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsqgcxpuq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsqgcxpuq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpugmyq6xl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpugmyq6xl/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpq2knshfk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq2knshfk/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdeshzm_i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdeshzm_i/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmppydwfacv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppydwfacv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfomu2nhp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfomu2nhp/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2r_570l2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2r_570l2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5ok50vhz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5ok50vhz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpw9csgddd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw9csgddd/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpg48pwetg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg48pwetg/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmps224rrz3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps224rrz3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9s0z5872/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9s0z5872/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp__nvfz6l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp__nvfz6l/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwd0tf1p2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwd0tf1p2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6h9ccqt7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6h9ccqt7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvwx401g_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvwx401g_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzp_jpoir/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzp_jpoir/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4clz__ra/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4clz__ra/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpigr048h6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpigr048h6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmporskmzbh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmporskmzbh/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpifaq4wi3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpifaq4wi3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmph1vujznl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph1vujznl/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqdp6rnqc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqdp6rnqc/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpeylbk47t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpeylbk47t/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmplgi4uocb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplgi4uocb/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmprbp25_xu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprbp25_xu/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjp6npqku/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjp6npqku/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgfersog8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgfersog8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkvjcqvgs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkvjcqvgs/f2.bed) ----------------------------- Captured stderr call ----------------------------- Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. ______________________ test_nearest[upstream-False-False] ______________________ [gw2] linux -- Python 3.12.6 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 880, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 323, in test_nearest | @pytest.mark.parametrize("nearest_how,overlap,strandedness", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1722, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 351, in test_nearest | result = gr.nearest( | ^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 292, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 115, in _nearest | r_idx, dist = _next_nonoverlapping(df_to_find_nearest_in.End, | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 62, in _next_nonoverlapping | r_idx, dist = nearest_next_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 34, in sorted_nearest.src.sorted_nearest.nearest_next_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_nearest( | nearest_how='upstream', | overlap=False, | strandedness=False, | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:101 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:110 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 | (and 40 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2TAAIyMmGIMAAB5AAQ=') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 351, in test_nearest | result = gr.nearest( | ^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 292, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 118, in _nearest | r_idx, dist = _previous_nonoverlapping(df_to_find_nearest_in.Start, | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_nearest( | nearest_how='upstream', | overlap=False, | strandedness=False, | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:101 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:118 | (and 39 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2TABIxYxAAAZAAD') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbltaxvra/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbltaxvra/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvrvbkw4w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvrvbkw4w/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7p23vb8d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7p23vb8d/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuyapx4i1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuyapx4i1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpq6hxnh3g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq6hxnh3g/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpd1xfmkje/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd1xfmkje/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6seer_ut/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6seer_ut/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwirsrhe6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwirsrhe6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdt2h0cp2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdt2h0cp2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9okrkm8v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9okrkm8v/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmi0lzqkq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmi0lzqkq/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_cgegt3d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_cgegt3d/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8wy8uqax/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8wy8uqax/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppgzqxlpk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppgzqxlpk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe8q53a27/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe8q53a27/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgs5ntk99/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgs5ntk99/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1lnbkt0j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1lnbkt0j/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3e9chi9z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3e9chi9z/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp75gkt3j6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp75gkt3j6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbz446kvw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbz446kvw/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplzyuko4h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplzyuko4h/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7su9x3a_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7su9x3a_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4oi04hsn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4oi04hsn/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5eg8_lda/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5eg8_lda/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkyo26v5g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkyo26v5g/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmponudn9kl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmponudn9kl/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpi8hosdn5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi8hosdn5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdicpivzy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdicpivzy/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpum55h_bg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpum55h_bg/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxie2f8hi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxie2f8hi/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_dtpmnu9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_dtpmnu9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsk3ptfae/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsk3ptfae/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnn1zt8l9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnn1zt8l9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjjh3me30/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjjh3me30/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxm9__mov/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxm9__mov/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpr_o9bsg4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr_o9bsg4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5h40urp8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5h40urp8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpi66xyk76/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi66xyk76/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmnda77m4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmnda77m4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp43qmr0n5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp43qmr0n5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5o504n_e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5o504n_e/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpj9cnqo3u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj9cnqo3u/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdui58d7c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdui58d7c/f2.bed) ___________ test_three_in_a_row[strandedness_chain58-method_chain58] ___________ [gw9] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', 'same') method_chain = ('set_intersect', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('set_intersect', 'overlap'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E (and 65 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2CAA0YGLAAAADUAAg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ___________ test_three_in_a_row[strandedness_chain10-method_chain10] ___________ [gw7] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', False) method_chain = ('set_intersect', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('set_intersect', 'nearest'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 E /usr/lib/python3/dist-packages/pandas/core/array_algos/take.py:574 E (and 61 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2DkKpucF6n0jIGRAQsAAEmUAuU=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ___________________ test_k_nearest[None-False-opposite-last] ___________________ [gw4] linux -- Python 3.12.6 /usr/bin/python3.12 nearest_how = None, overlap = False, strandedness = 'opposite', ties = 'last' @pytest.mark.bedtools > @pytest.mark.explore tests/test_binary.py:510: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:548: in test_k_nearest result = gr.k_nearest( pyranges/pyranges.py:2450: in k_nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/k_nearest.py:180: in _nearest df = __nearest(d1, d2, **kwargs) pyranges/methods/k_nearest.py:71: in nearest plidx, pridx, pdist = nearest_previous_idx(d1, d2, d1.__k__.values, ties) pyranges/methods/k_nearest.py:28: in nearest_previous_idx lidx, ridx_pos, dist = k_nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_k_nearest( E nearest_how=None, E overlap=False, E strandedness='opposite', E ties='last', E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr2 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr2 | 1 | 2 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:14 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:15 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:160 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:19 E (and 38 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2SAAEYGBGDEFGMEAACRAAY=') as a decorator on your test case sorted_nearest/src/k_nearest.pyx:28: ValueError ----------------------------- Captured stdout call ----------------------------- ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5i5j8xvv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5i5j8xvv/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgvot__v1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgvot__v1/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwbaiqy40/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwbaiqy40/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpm69i7tj8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm69i7tj8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9amjc3ld/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9amjc3ld/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpz8murph9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz8murph9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpimrdb4rn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpimrdb4rn/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4zbh_v5t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4zbh_v5t/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvfob4izo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvfob4izo/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpt1o9dvq0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt1o9dvq0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbqhw13j1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbqhw13j1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0prnbwo0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0prnbwo0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0ryrwbxn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0ryrwbxn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpma4fkfbc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpma4fkfbc/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpa34xr0rv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa34xr0rv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcxozy4td/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcxozy4td/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpf8fs2tgo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf8fs2tgo/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpo_vg81s0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo_vg81s0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzq4o_m6_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzq4o_m6_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnalxu9ns/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnalxu9ns/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpq04u28zt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq04u28zt/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpn1g8bjxz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn1g8bjxz/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9_zw7hv1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9_zw7hv1/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp34rrgufw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp34rrgufw/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvd9dj75v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvd9dj75v/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp706q5pde/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp706q5pde/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdr2alryi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdr2alryi/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9opdl4pf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9opdl4pf/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5jzge0gt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5jzge0gt/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4z87q2s8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4z87q2s8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_kvbs9p_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_kvbs9p_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvd_9wuqa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvd_9wuqa/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpve7tl19h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpve7tl19h/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7vml2lrg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7vml2lrg/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmph0qyg91i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph0qyg91i/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmprmmp4r4h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprmmp4r4h/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp08z15oho/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp08z15oho/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwlpf8c3p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwlpf8c3p/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpc9kk9040/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc9kk9040/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmplfi7yfqe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplfi7yfqe/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpo87baxll/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo87baxll/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmphvymrkjj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphvymrkjj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5li3fd6y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5li3fd6y/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmplutrfu9l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplutrfu9l/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8hbe3mwz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8hbe3mwz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfr4z3w36/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfr4z3w36/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_e3os0dw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_e3os0dw/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1_ghowk4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1_ghowk4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdgb24snb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdgb24snb/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmppdmk17dq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppdmk17dq/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1tsldhm_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1tsldhm_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmprso4rasn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprso4rasn/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwlapent_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwlapent_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5frct_mc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5frct_mc/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpne7iigvz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpne7iigvz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5zl32jnx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5zl32jnx/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpduew_k99/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpduew_k99/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqa73s59t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqa73s59t/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp86l0wnvd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp86l0wnvd/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpiss02l2t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiss02l2t/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpv244cz7t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv244cz7t/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwav2b0x3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwav2b0x3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmplgojw6je/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplgojw6je/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7qhvheg8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7qhvheg8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwesw4j5e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwesw4j5e/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpd09tjp0b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd09tjp0b/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpn2mcf6li/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn2mcf6li/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyiuw8d08/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyiuw8d08/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0ixgoano/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0ixgoano/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnwi02cva/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnwi02cva/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_4wmtwez/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_4wmtwez/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjoyuhlsd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjoyuhlsd/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8wl44stu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8wl44stu/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdg14x3tp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdg14x3tp/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzq0hn91o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzq0hn91o/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmptzympwxe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptzympwxe/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsubctagc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsubctagc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpchb4jxkz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpchb4jxkz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmppxh4ioh9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppxh4ioh9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpeyigotra/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpeyigotra/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2cfjmy2z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2cfjmy2z/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbsv0kuvm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbsv0kuvm/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1i4ehcef/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1i4ehcef/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpudiz_0zp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpudiz_0zp/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyoo9la82/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyoo9la82/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzk1tmfng/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzk1tmfng/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbxdlgss9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbxdlgss9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnwcveh6g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnwcveh6g/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9_1e0l0u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9_1e0l0u/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpo81sgai9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo81sgai9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvls5wsro/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvls5wsro/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7w7u7t_z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7w7u7t_z/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpztgpfrv7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpztgpfrv7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp36157fn6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp36157fn6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1phspco7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1phspco7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0peps39n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0peps39n/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpz696v4p3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz696v4p3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwbf_m7k5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwbf_m7k5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkf63z53q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkf63z53q/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp834h47_g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp834h47_g/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpv3n4tnw8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv3n4tnw8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcnda6u_s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcnda6u_s/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmppfi0lv6v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppfi0lv6v/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp00dlrqnw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp00dlrqnw/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6lwquo3m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6lwquo3m/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmlgde7uc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmlgde7uc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzc4wqhmp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzc4wqhmp/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1foxg03r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1foxg03r/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpejaubt8g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpejaubt8g/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5y3nuc51/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5y3nuc51/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsj1iyaer/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsj1iyaer/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpj2p0iwwd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj2p0iwwd/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpq1qhway7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq1qhway7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfzu9cqyy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfzu9cqyy/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzrqtyt00/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzrqtyt00/f2.bed) ----------------------------- Captured stderr call ----------------------------- Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr4 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr4 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. ___________ test_three_in_a_row[strandedness_chain47-method_chain47] ___________ [gw10] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', False), method_chain = ('join', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('join', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:15 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:145 E (and 24 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ___________ test_three_in_a_row[strandedness_chain35-method_chain35] ___________ [gw8] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', False), method_chain = ('subtract', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('subtract', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:112 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:117 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 E (and 132 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2DUj97HYC7HwcjAyIAJACyfAak=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') _____________________ test_k_nearest[None-False-same-last] _____________________ [gw4] linux -- Python 3.12.6 /usr/bin/python3.12 nearest_how = None, overlap = False, strandedness = 'same', ties = 'last' @pytest.mark.bedtools > @pytest.mark.explore tests/test_binary.py:510: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:548: in test_k_nearest result = gr.k_nearest( pyranges/pyranges.py:2450: in k_nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/k_nearest.py:180: in _nearest df = __nearest(d1, d2, **kwargs) pyranges/methods/k_nearest.py:71: in nearest plidx, pridx, pdist = nearest_previous_idx(d1, d2, d1.__k__.values, ties) pyranges/methods/k_nearest.py:28: in nearest_previous_idx lidx, ridx_pos, dist = k_nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_k_nearest( E nearest_how=None, E overlap=False, E strandedness='same', E ties='last', E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:14 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:15 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:160 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:19 E (and 38 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2TABIxYxAAAZAAD') as a decorator on your test case sorted_nearest/src/k_nearest.pyx:28: ValueError ----------------------------- Captured stdout call ----------------------------- ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpk9l120bs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk9l120bs/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1tjjq5em/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1tjjq5em/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpr9i_z4gm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr9i_z4gm/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7j5ddxpu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7j5ddxpu/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3h20166s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3h20166s/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpucwcctp2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpucwcctp2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbmlm4sml/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbmlm4sml/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5v220od1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5v220od1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4h6kcgo7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4h6kcgo7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp68c1fb0k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp68c1fb0k/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp169q2j6v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp169q2j6v/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp56imb053/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp56imb053/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbrqyscpv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbrqyscpv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8s4o504c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8s4o504c/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpplx5weyb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpplx5weyb/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7xtoyf8b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7xtoyf8b/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp831hwjfv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp831hwjfv/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpa53wjjfa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa53wjjfa/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8wph7eew/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8wph7eew/f2.bed) ----------------------------- Captured stderr call ----------------------------- Warning: Fewer hits (1) found on chr17 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr7 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr7 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr7 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr7 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr10 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr10 than requested (2). It is likely that there are fewer total records on that chromosome than requested. ______________________ test_nearest[upstream-False-same] _______________________ [gw2] linux -- Python 3.12.6 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 880, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 323, in test_nearest | @pytest.mark.parametrize("nearest_how,overlap,strandedness", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1722, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 351, in test_nearest | result = gr.nearest( | ^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 118, in _nearest | r_idx, dist = _previous_nonoverlapping(df_to_find_nearest_in.Start, | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_nearest( | nearest_how='upstream', | overlap=False, | strandedness='same', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | (and 103 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2TABIxYxAAAZAAD') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 351, in test_nearest | result = gr.nearest( | ^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 115, in _nearest | r_idx, dist = _next_nonoverlapping(df_to_find_nearest_in.End, | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 62, in _next_nonoverlapping | r_idx, dist = nearest_next_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 34, in sorted_nearest.src.sorted_nearest.nearest_next_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_nearest( | nearest_how='upstream', | overlap=False, | strandedness='same', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | (and 103 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2TAAIyMUBpJCAAAggAG') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpc75eix3u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc75eix3u/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmps40dzgi0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps40dzgi0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkt1kz0uh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkt1kz0uh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpatp252u6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpatp252u6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp25a7mo7n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp25a7mo7n/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwys0rm2d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwys0rm2d/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7pbzrasr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7pbzrasr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp13i55uyu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp13i55uyu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzqtryvp3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzqtryvp3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpto051mxh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpto051mxh/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvv3ztk2n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvv3ztk2n/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpa971wiwf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa971wiwf/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5ksvg7m7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5ksvg7m7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwzt83d7i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwzt83d7i/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqhr8l87y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqhr8l87y/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpd3xd9p4_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd3xd9p4_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2hjp9rhz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2hjp9rhz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmsic1vrx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmsic1vrx/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_jf8318g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_jf8318g/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpomvxb5_o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpomvxb5_o/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpn4kgpc2m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn4kgpc2m/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcu0v49t5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcu0v49t5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmparhzuiq4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmparhzuiq4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5prco4mu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5prco4mu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6exv1stk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6exv1stk/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpauwb5rb6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpauwb5rb6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzeux67si/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzeux67si/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp16umlcp6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp16umlcp6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppj07_4sd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppj07_4sd/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcfh2df8w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcfh2df8w/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpo_m7yyje/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo_m7yyje/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphjdpgu8b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphjdpgu8b/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1sna2wg6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1sna2wg6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpk21rhdm_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk21rhdm_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpur1lfs6f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpur1lfs6f/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcpwgjtae/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcpwgjtae/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdntwwcl9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdntwwcl9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpj222pf4z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj222pf4z/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpj5kow8hf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj5kow8hf/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyzf30v8d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyzf30v8d/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpefqvs0b0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpefqvs0b0/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp62nj_tff/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp62nj_tff/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7ut_ej1b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7ut_ej1b/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsc5uvjz4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsc5uvjz4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpx6xwuz23/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx6xwuz23/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpi3zune4z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi3zune4z/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpy4vxbzgt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy4vxbzgt/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpg_2naq9w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg_2naq9w/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpc9zuj2dv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc9zuj2dv/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpobt651c3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpobt651c3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpayzr4tbg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpayzr4tbg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4e3in_zj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4e3in_zj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpd5hubbr8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd5hubbr8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwrzqvtjk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwrzqvtjk/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp56n4skyi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp56n4skyi/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphlz64pio/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphlz64pio/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppvg9oudf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppvg9oudf/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3k9o2zsw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3k9o2zsw/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpd83gfmrb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd83gfmrb/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpofkskn_g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpofkskn_g/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvvh3cfoh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvvh3cfoh/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqidgov2b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqidgov2b/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpz8nkt0_a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz8nkt0_a/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpoq7dq02e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoq7dq02e/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphsj34hvf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphsj34hvf/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp12k24u7d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp12k24u7d/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpx7aw0yrr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx7aw0yrr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7yp6y5gx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7yp6y5gx/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwdf0l9e3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwdf0l9e3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp761zoels/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp761zoels/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8ogs_sil/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8ogs_sil/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsvh7zij2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsvh7zij2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwvks5ffz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwvks5ffz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqzik1iru/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqzik1iru/f2.bed) ____________ test_three_in_a_row[strandedness_chain3-method_chain3] ____________ [gw5] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', False), method_chain = ('set_union', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('set_union', 'nearest'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E (and 179 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2CUK/BPMOTYw8jIgAUAADiQAjY=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 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'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ___________ test_three_in_a_row[strandedness_chain22-method_chain22] ___________ [gw6] linux -- Python 3.12.6 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 880, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1722, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', False), | method_chain=('nearest', 'set_intersect'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=Empty PyRanges, | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | (and 173 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2RAAowoFC4AAACrAAQ=') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3688, in set_intersect | other_clusters = other.merge(strand=strand) | ^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 381, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', False), | method_chain=('nearest', 'set_intersect'), | gr=Empty PyRanges, | gr2=Empty PyRanges, # or any other generated value | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:38 | (and 165 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain59-method_chain59] ___________ [gw9] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', 'same') method_chain = ('set_intersect', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('set_intersect', 'nearest'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 E /usr/lib/python3/dist-packages/pandas/core/array_algos/take.py:574 E (and 61 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2CAA0YGLAAAADUAAg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ____________________ test_k_nearest[None-False-False-last] _____________________ [gw4] linux -- Python 3.12.6 /usr/bin/python3.12 nearest_how = None, overlap = False, strandedness = False, ties = 'last' @pytest.mark.bedtools > @pytest.mark.explore tests/test_binary.py:510: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:548: in test_k_nearest result = gr.k_nearest( pyranges/pyranges.py:2450: in k_nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:292: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/k_nearest.py:180: in _nearest df = __nearest(d1, d2, **kwargs) pyranges/methods/k_nearest.py:71: in nearest plidx, pridx, pdist = nearest_previous_idx(d1, d2, d1.__k__.values, ties) pyranges/methods/k_nearest.py:28: in nearest_previous_idx lidx, ridx_pos, dist = k_nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_k_nearest( E nearest_how=None, E overlap=False, E strandedness=False, E ties='last', E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:14 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:15 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:160 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:19 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:28 E (and 35 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2TABIxYxAAAZAAD') as a decorator on your test case sorted_nearest/src/k_nearest.pyx:28: ValueError ----------------------------- Captured stdout call ----------------------------- ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp82_88yjv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp82_88yjv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqwlo45k3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqwlo45k3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpn5bhhqhd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn5bhhqhd/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmut1okv_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmut1okv_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwiw05z8s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwiw05z8s/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5s1v595r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5s1v595r/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgvlwse17/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgvlwse17/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpj69y5pe0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj69y5pe0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpiktgufqs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiktgufqs/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp298fqvfo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp298fqvfo/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6zm1r1we/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6zm1r1we/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpw6opri3v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw6opri3v/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpz_xfc06h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz_xfc06h/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfxwa01c6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfxwa01c6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4idkh3aa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4idkh3aa/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7n_t1myk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7n_t1myk/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpaoapvg8z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaoapvg8z/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8f0b_rui/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8f0b_rui/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmplfr1fpas/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplfr1fpas/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpx_835d3i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx_835d3i/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmppnnw6v87/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppnnw6v87/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_g7sp1im/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_g7sp1im/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzoyzn3x6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzoyzn3x6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdb6037d5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdb6037d5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0lyu812d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0lyu812d/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmptkb5ahok/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptkb5ahok/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7o1br6gr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7o1br6gr/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxkemphy3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxkemphy3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4b67d3ln/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4b67d3ln/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuzqvmwr4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuzqvmwr4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2zzlrj_6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2zzlrj_6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmplh0i4c69/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplh0i4c69/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpc9l_92re/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc9l_92re/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7c7p1v5a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7c7p1v5a/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpo0jp0pa6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo0jp0pa6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp809mb1pa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp809mb1pa/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdhowr7wy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdhowr7wy/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp62g9m746/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp62g9m746/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp40oubag3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp40oubag3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpy3uzduy9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy3uzduy9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnnv26zlb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnnv26zlb/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvb1js6m8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvb1js6m8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnhsk7ml0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnhsk7ml0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfkgwlwq_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfkgwlwq_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp63e_nz8a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp63e_nz8a/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpj0077kve/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj0077kve/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_3jqgaye/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_3jqgaye/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3ry65y0p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3ry65y0p/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpa8xomxu2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa8xomxu2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwreqa0rx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwreqa0rx/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjoc9zbx9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjoc9zbx9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdn1uh630/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdn1uh630/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8mgdr2vb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8mgdr2vb/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmppj2xd6ul/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppj2xd6ul/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmppwkpm6yu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppwkpm6yu/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5my9dkoz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5my9dkoz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmppauti5nj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppauti5nj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp43i40qdn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp43i40qdn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpz97y5ume/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz97y5ume/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5f14kt88/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5f14kt88/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8bzz9c2h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8bzz9c2h/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3vyjsfqg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3vyjsfqg/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpugebn937/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpugebn937/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbt6c1q4r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbt6c1q4r/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpadbil9wg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpadbil9wg/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuzbfoz2c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuzbfoz2c/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6058ldnl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6058ldnl/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwqdl3tht/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwqdl3tht/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwcllv7jl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwcllv7jl/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8lq0fi1a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8lq0fi1a/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyh8qm307/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyh8qm307/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp872206xr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp872206xr/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5mqscz4m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5mqscz4m/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyagek8nv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyagek8nv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwd8_6zwl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwd8_6zwl/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnic8pk5g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnic8pk5g/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmps_6p2vuh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps_6p2vuh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpznobg3hy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpznobg3hy/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpj0z7d973/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj0z7d973/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9h47mapg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9h47mapg/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkuuq8xni/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkuuq8xni/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpiap17kok/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiap17kok/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpe9hgxsq5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe9hgxsq5/f2.bed) ----------------------------- Captured stderr call ----------------------------- Warning: Fewer hits (1) found on chr18 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrX than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrX than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. ____________________________ test_subtraction[same] ____________________________ [gw1] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness = 'same' @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness", ["same", "opposite", False]) # tests/test_binary.py:286: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:308: in test_subtraction result = gr.subtract(gr2, strandedness=strandedness) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_subtraction( E # The test always failed when commented parts were varied together. E strandedness='same', E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., # or any other generated value E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., # or any other generated value E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2TABIxYxAAAZAAD') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp77ob_kih/f1.bed -b /tmp/tmp77ob_kih/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpdkdh1s6g/f1.bed -b /tmp/tmpdkdh1s6g/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpoo1ign1n/f1.bed -b /tmp/tmpoo1ign1n/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpboga_8a3/f1.bed -b /tmp/tmpboga_8a3/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpchhu_4zx/f1.bed -b /tmp/tmpchhu_4zx/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpiowxextm/f1.bed -b /tmp/tmpiowxextm/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmphwawa37_/f1.bed -b /tmp/tmphwawa37_/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmppju52l1o/f1.bed -b /tmp/tmppju52l1o/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpo0lu6epu/f1.bed -b /tmp/tmpo0lu6epu/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp0k9nk72t/f1.bed -b /tmp/tmp0k9nk72t/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpcmamwszh/f1.bed -b /tmp/tmpcmamwszh/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpmxgnsu8g/f1.bed -b /tmp/tmpmxgnsu8g/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp9gi_1uep/f1.bed -b /tmp/tmp9gi_1uep/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpta8bgixq/f1.bed -b /tmp/tmpta8bgixq/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpbv8mrefa/f1.bed -b /tmp/tmpbv8mrefa/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmphfkm2n1o/f1.bed -b /tmp/tmphfkm2n1o/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp1lqx8q89/f1.bed -b /tmp/tmp1lqx8q89/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpk5ogem97/f1.bed -b /tmp/tmpk5ogem97/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp7vp07mn4/f1.bed -b /tmp/tmp7vp07mn4/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpdlq1n55z/f1.bed -b /tmp/tmpdlq1n55z/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpsp6rft9h/f1.bed -b /tmp/tmpsp6rft9h/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpm1boxph6/f1.bed -b /tmp/tmpm1boxph6/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpc04r_k1t/f1.bed -b /tmp/tmpc04r_k1t/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpxla6os8m/f1.bed -b /tmp/tmpxla6os8m/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpledv6iko/f1.bed -b /tmp/tmpledv6iko/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpq6fygamk/f1.bed -b /tmp/tmpq6fygamk/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpjx__w9og/f1.bed -b /tmp/tmpjx__w9og/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmphtplu_e1/f1.bed -b /tmp/tmphtplu_e1/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpo7hgusde/f1.bed -b /tmp/tmpo7hgusde/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpjz3si8ep/f1.bed -b /tmp/tmpjz3si8ep/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpyra51mt2/f1.bed -b /tmp/tmpyra51mt2/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmprhlu88hk/f1.bed -b /tmp/tmprhlu88hk/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmprq8oafei/f1.bed -b /tmp/tmprq8oafei/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpmq0edob5/f1.bed -b /tmp/tmpmq0edob5/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpc26mogvm/f1.bed -b /tmp/tmpc26mogvm/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp152n4uqj/f1.bed -b /tmp/tmp152n4uqj/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpff954v2e/f1.bed -b /tmp/tmpff954v2e/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpeapyuwgt/f1.bed -b /tmp/tmpeapyuwgt/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpsdx2s88d/f1.bed -b /tmp/tmpsdx2s88d/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpxmngagrg/f1.bed -b /tmp/tmpxmngagrg/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp83l_z43c/f1.bed -b /tmp/tmp83l_z43c/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpp8aagr8y/f1.bed -b /tmp/tmpp8aagr8y/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp4gzljl3g/f1.bed -b /tmp/tmp4gzljl3g/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpezo0xyac/f1.bed -b /tmp/tmpezo0xyac/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpvxwgxky8/f1.bed -b /tmp/tmpvxwgxky8/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp_llxt1l4/f1.bed -b /tmp/tmp_llxt1l4/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpxaionqy3/f1.bed -b /tmp/tmpxaionqy3/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpmny8x1za/f1.bed -b /tmp/tmpmny8x1za/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmppw00c5c2/f1.bed -b /tmp/tmppw00c5c2/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpa2qdkjtm/f1.bed -b /tmp/tmpa2qdkjtm/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmprj7udsab/f1.bed -b /tmp/tmprj7udsab/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpbejbd1c3/f1.bed -b /tmp/tmpbejbd1c3/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmproz0neqc/f1.bed -b /tmp/tmproz0neqc/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp4d1wwjus/f1.bed -b /tmp/tmp4d1wwjus/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpsutci16j/f1.bed -b /tmp/tmpsutci16j/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmppf1fri84/f1.bed -b /tmp/tmppf1fri84/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp52epnf49/f1.bed -b /tmp/tmp52epnf49/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmph2i4f27s/f1.bed -b /tmp/tmph2i4f27s/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpqu78it6e/f1.bed -b /tmp/tmpqu78it6e/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpvgh_eylm/f1.bed -b /tmp/tmpvgh_eylm/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp42di40c_/f1.bed -b /tmp/tmp42di40c_/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpmaowqdtk/f1.bed -b /tmp/tmpmaowqdtk/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp85kyqrkr/f1.bed -b /tmp/tmp85kyqrkr/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp6g2f11ce/f1.bed -b /tmp/tmp6g2f11ce/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpv6bzhv7q/f1.bed -b /tmp/tmpv6bzhv7q/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpp06kcjga/f1.bed -b /tmp/tmpp06kcjga/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp47xeov5x/f1.bed -b /tmp/tmp47xeov5x/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp4e90p7jl/f1.bed -b /tmp/tmp4e90p7jl/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpz_cofk52/f1.bed -b /tmp/tmpz_cofk52/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp1p3mrifw/f1.bed -b /tmp/tmp1p3mrifw/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpkbfa2y8z/f1.bed -b /tmp/tmpkbfa2y8z/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp30xj8hus/f1.bed -b /tmp/tmp30xj8hus/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp20vkjimc/f1.bed -b /tmp/tmp20vkjimc/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpl88aserr/f1.bed -b /tmp/tmpl88aserr/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp6n12zk0m/f1.bed -b /tmp/tmp6n12zk0m/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpo127ty7a/f1.bed -b /tmp/tmpo127ty7a/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp3x0vu12j/f1.bed -b /tmp/tmp3x0vu12j/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp3jnttsr3/f1.bed -b /tmp/tmp3jnttsr3/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmplf9bpwha/f1.bed -b /tmp/tmplf9bpwha/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpvg8liw5_/f1.bed -b /tmp/tmpvg8liw5_/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp94cvhe_e/f1.bed -b /tmp/tmp94cvhe_e/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp6yxmh4ft/f1.bed -b /tmp/tmp6yxmh4ft/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpqrc6jfd8/f1.bed -b /tmp/tmpqrc6jfd8/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpk5f1yjxg/f1.bed -b /tmp/tmpk5f1yjxg/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpvz820h14/f1.bed -b /tmp/tmpvz820h14/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp6yy5edor/f1.bed -b /tmp/tmp6yy5edor/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpon6meilb/f1.bed -b /tmp/tmpon6meilb/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpukkjzvxu/f1.bed -b /tmp/tmpukkjzvxu/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpjrnsfr5y/f1.bed -b /tmp/tmpjrnsfr5y/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpszzr0v7i/f1.bed -b /tmp/tmpszzr0v7i/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp810ny_np/f1.bed -b /tmp/tmp810ny_np/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpr2le6n_i/f1.bed -b /tmp/tmpr2le6n_i/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp6exgacez/f1.bed -b /tmp/tmp6exgacez/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpig8rl1r4/f1.bed -b /tmp/tmpig8rl1r4/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpimms422z/f1.bed -b /tmp/tmpimms422z/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpy2tn3brd/f1.bed -b /tmp/tmpy2tn3brd/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpjke74r9j/f1.bed -b /tmp/tmpjke74r9j/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpzwtxb7sc/f1.bed -b /tmp/tmpzwtxb7sc/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp0lgbkvge/f1.bed -b /tmp/tmp0lgbkvge/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpijsev6_l/f1.bed -b /tmp/tmpijsev6_l/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp_cz55tg3/f1.bed -b /tmp/tmp_cz55tg3/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpze9fqq6b/f1.bed -b /tmp/tmpze9fqq6b/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp8s3njiwc/f1.bed -b /tmp/tmp8s3njiwc/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpvthwykb4/f1.bed -b /tmp/tmpvthwykb4/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpjm3rbrrn/f1.bed -b /tmp/tmpjm3rbrrn/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpi7w4czmz/f1.bed -b /tmp/tmpi7w4czmz/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp8rrv9v96/f1.bed -b /tmp/tmp8rrv9v96/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpokf2lbax/f1.bed -b /tmp/tmpokf2lbax/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp6etc5vda/f1.bed -b /tmp/tmp6etc5vda/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp10zotx87/f1.bed -b /tmp/tmp10zotx87/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpahufa996/f1.bed -b /tmp/tmpahufa996/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp5i4e9cob/f1.bed -b /tmp/tmp5i4e9cob/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmppg_03x2q/f1.bed -b /tmp/tmppg_03x2q/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpt31mbceg/f1.bed -b /tmp/tmpt31mbceg/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp__qrder6/f1.bed -b /tmp/tmp__qrder6/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpjs1cph96/f1.bed -b /tmp/tmpjs1cph96/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp3artb55m/f1.bed -b /tmp/tmp3artb55m/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpqu3c6wo7/f1.bed -b /tmp/tmpqu3c6wo7/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpnbsdr9y9/f1.bed -b /tmp/tmpnbsdr9y9/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp55tady7h/f1.bed -b /tmp/tmp55tady7h/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpg3nongse/f1.bed -b /tmp/tmpg3nongse/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp_z3hd1ar/f1.bed -b /tmp/tmp_z3hd1ar/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpa24mhjph/f1.bed -b /tmp/tmpa24mhjph/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp4ykn0bez/f1.bed -b /tmp/tmp4ykn0bez/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp52efvetw/f1.bed -b /tmp/tmp52efvetw/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp4ch4mn7j/f1.bed -b /tmp/tmp4ch4mn7j/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmprdi7d7zw/f1.bed -b /tmp/tmprdi7d7zw/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpki2uzcn0/f1.bed -b /tmp/tmpki2uzcn0/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmptzcucz5d/f1.bed -b /tmp/tmptzcucz5d/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpa9toyvp1/f1.bed -b /tmp/tmpa9toyvp1/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpr7c8osb7/f1.bed -b /tmp/tmpr7c8osb7/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpz7j0r5_c/f1.bed -b /tmp/tmpz7j0r5_c/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp_g12dd3i/f1.bed -b /tmp/tmp_g12dd3i/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpzpzhtwk4/f1.bed -b /tmp/tmpzpzhtwk4/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpw5yrkdr8/f1.bed -b /tmp/tmpw5yrkdr8/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpl3m16ftj/f1.bed -b /tmp/tmpl3m16ftj/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp1g4sq1z4/f1.bed -b /tmp/tmp1g4sq1z4/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp1okyp62b/f1.bed -b /tmp/tmp1okyp62b/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpgo2puhw7/f1.bed -b /tmp/tmpgo2puhw7/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp2epcys6k/f1.bed -b /tmp/tmp2epcys6k/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpqpekg_gn/f1.bed -b /tmp/tmpqpekg_gn/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpb2spp9vc/f1.bed -b /tmp/tmpb2spp9vc/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpikbhl0cx/f1.bed -b /tmp/tmpikbhl0cx/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpa7q2lhu8/f1.bed -b /tmp/tmpa7q2lhu8/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpss5i92uw/f1.bed -b /tmp/tmpss5i92uw/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmprekyruuh/f1.bed -b /tmp/tmprekyruuh/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmphnowqjb5/f1.bed -b /tmp/tmphnowqjb5/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpohz0f12v/f1.bed -b /tmp/tmpohz0f12v/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp9bhgw5er/f1.bed -b /tmp/tmp9bhgw5er/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpvqq6xm5x/f1.bed -b /tmp/tmpvqq6xm5x/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpcw5myb9i/f1.bed -b /tmp/tmpcw5myb9i/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpstsqnn9m/f1.bed -b /tmp/tmpstsqnn9m/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpbjd4a17m/f1.bed -b /tmp/tmpbjd4a17m/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpawu0c35o/f1.bed -b /tmp/tmpawu0c35o/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpgpv73y8u/f1.bed -b /tmp/tmpgpv73y8u/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp0_bf2mry/f1.bed -b /tmp/tmp0_bf2mry/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpto_1u38f/f1.bed -b /tmp/tmpto_1u38f/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpnto8cs9w/f1.bed -b /tmp/tmpnto8cs9w/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpyb3y89z5/f1.bed -b /tmp/tmpyb3y89z5/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpa9hia5ze/f1.bed -b /tmp/tmpa9hia5ze/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp8l83elsj/f1.bed -b /tmp/tmp8l83elsj/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpj9hzp1d0/f1.bed -b /tmp/tmpj9hzp1d0/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpvbode3ye/f1.bed -b /tmp/tmpvbode3ye/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpj0wln4uh/f1.bed -b /tmp/tmpj0wln4uh/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp2bjdw1m7/f1.bed -b /tmp/tmp2bjdw1m7/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpa8wb60bg/f1.bed -b /tmp/tmpa8wb60bg/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp5l46loxl/f1.bed -b /tmp/tmp5l46loxl/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpaoj35cyu/f1.bed -b /tmp/tmpaoj35cyu/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpuf5bsiro/f1.bed -b /tmp/tmpuf5bsiro/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp1f1aekhj/f1.bed -b /tmp/tmp1f1aekhj/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp9r7je34d/f1.bed -b /tmp/tmp9r7je34d/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpegog6cvr/f1.bed -b /tmp/tmpegog6cvr/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpeczdpwp6/f1.bed -b /tmp/tmpeczdpwp6/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp9cbxw5ap/f1.bed -b /tmp/tmp9cbxw5ap/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpzem_fnff/f1.bed -b /tmp/tmpzem_fnff/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpder_m__u/f1.bed -b /tmp/tmpder_m__u/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpzeq95tc9/f1.bed -b /tmp/tmpzeq95tc9/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpz9sfct4b/f1.bed -b /tmp/tmpz9sfct4b/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpwmepegwd/f1.bed -b /tmp/tmpwmepegwd/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpkj8pv2v0/f1.bed -b /tmp/tmpkj8pv2v0/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpxqo1ind7/f1.bed -b /tmp/tmpxqo1ind7/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp241jq730/f1.bed -b /tmp/tmp241jq730/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpjcyafixp/f1.bed -b /tmp/tmpjcyafixp/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpvena0zr5/f1.bed -b /tmp/tmpvena0zr5/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp1rww_gl3/f1.bed -b /tmp/tmp1rww_gl3/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp2j60f6wy/f1.bed -b /tmp/tmp2j60f6wy/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmplg9fxs3b/f1.bed -b /tmp/tmplg9fxs3b/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpytib64yi/f1.bed -b /tmp/tmpytib64yi/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmptgdjm8bu/f1.bed -b /tmp/tmptgdjm8bu/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmppqy3xbib/f1.bed -b /tmp/tmppqy3xbib/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpuhaz383t/f1.bed -b /tmp/tmpuhaz383t/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpvfwh3kq7/f1.bed -b /tmp/tmpvfwh3kq7/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpwikmkj9k/f1.bed -b /tmp/tmpwikmkj9k/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpjwuoso9v/f1.bed -b /tmp/tmpjwuoso9v/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpk3tjzcsd/f1.bed -b /tmp/tmpk3tjzcsd/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp9dizuoud/f1.bed -b /tmp/tmp9dizuoud/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp2nkgowrg/f1.bed -b /tmp/tmp2nkgowrg/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpeo0qzjsz/f1.bed -b /tmp/tmpeo0qzjsz/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpdfri6pp0/f1.bed -b /tmp/tmpdfri6pp0/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpa0e0tv2_/f1.bed -b /tmp/tmpa0e0tv2_/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmppudhbh4_/f1.bed -b /tmp/tmppudhbh4_/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp436k9d2e/f1.bed -b /tmp/tmp436k9d2e/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmplqe20l_z/f1.bed -b /tmp/tmplqe20l_z/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpmovc80t6/f1.bed -b /tmp/tmpmovc80t6/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp7qetz33k/f1.bed -b /tmp/tmp7qetz33k/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp41cunj01/f1.bed -b /tmp/tmp41cunj01/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpjc062ul8/f1.bed -b /tmp/tmpjc062ul8/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp6aicx7lj/f1.bed -b /tmp/tmp6aicx7lj/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpny91t5w4/f1.bed -b /tmp/tmpny91t5w4/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpu773duhb/f1.bed -b /tmp/tmpu773duhb/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpktmy3bsy/f1.bed -b /tmp/tmpktmy3bsy/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp0x3b2dzn/f1.bed -b /tmp/tmp0x3b2dzn/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpwjgln9xd/f1.bed -b /tmp/tmpwjgln9xd/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp4m74i358/f1.bed -b /tmp/tmp4m74i358/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpl_wspw87/f1.bed -b /tmp/tmpl_wspw87/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpik42w3sy/f1.bed -b /tmp/tmpik42w3sy/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpgtcanh9h/f1.bed -b /tmp/tmpgtcanh9h/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp1x42qn3_/f1.bed -b /tmp/tmp1x42qn3_/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp_ne7hoe8/f1.bed -b /tmp/tmp_ne7hoe8/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpz4qnmbcq/f1.bed -b /tmp/tmpz4qnmbcq/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpkvxy_tem/f1.bed -b /tmp/tmpkvxy_tem/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpjat_135t/f1.bed -b /tmp/tmpjat_135t/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpejqbnhji/f1.bed -b /tmp/tmpejqbnhji/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpjo4fr31p/f1.bed -b /tmp/tmpjo4fr31p/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmprpv_aivd/f1.bed -b /tmp/tmprpv_aivd/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpkgnojcb2/f1.bed -b /tmp/tmpkgnojcb2/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp0wonmaga/f1.bed -b /tmp/tmp0wonmaga/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpvn340wby/f1.bed -b /tmp/tmpvn340wby/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp7nrilsk8/f1.bed -b /tmp/tmp7nrilsk8/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp_omfwse6/f1.bed -b /tmp/tmp_omfwse6/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp6db6lo_g/f1.bed -b /tmp/tmp6db6lo_g/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpp_xoo8v_/f1.bed -b /tmp/tmpp_xoo8v_/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp8i4mn4ea/f1.bed -b /tmp/tmp8i4mn4ea/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpxy8rm7a2/f1.bed -b /tmp/tmpxy8rm7a2/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpi1rh7b60/f1.bed -b /tmp/tmpi1rh7b60/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpaawhsbq1/f1.bed -b /tmp/tmpaawhsbq1/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpnxohmczy/f1.bed -b /tmp/tmpnxohmczy/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp3mahwb0k/f1.bed -b /tmp/tmp3mahwb0k/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpwadubcig/f1.bed -b /tmp/tmpwadubcig/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpzz9cgx_a/f1.bed -b /tmp/tmpzz9cgx_a/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpmi5eb3jd/f1.bed -b /tmp/tmpmi5eb3jd/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpoll7xd0u/f1.bed -b /tmp/tmpoll7xd0u/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpu7jrnsju/f1.bed -b /tmp/tmpu7jrnsju/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpo2rw788p/f1.bed -b /tmp/tmpo2rw788p/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpw0gbj08r/f1.bed -b /tmp/tmpw0gbj08r/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpn76sgxe9/f1.bed -b /tmp/tmpn76sgxe9/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp9pgfszjn/f1.bed -b /tmp/tmp9pgfszjn/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpgg88tfc2/f1.bed -b /tmp/tmpgg88tfc2/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpzdscxyoy/f1.bed -b /tmp/tmpzdscxyoy/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp0qjfy6fv/f1.bed -b /tmp/tmp0qjfy6fv/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpf9zpxe1j/f1.bed -b /tmp/tmpf9zpxe1j/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpmvfutjju/f1.bed -b /tmp/tmpmvfutjju/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmprharq5ya/f1.bed -b /tmp/tmprharq5ya/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpwzqkaeio/f1.bed -b /tmp/tmpwzqkaeio/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpzekji774/f1.bed -b /tmp/tmpzekji774/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp7htrxvot/f1.bed -b /tmp/tmp7htrxvot/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpslx8q4hn/f1.bed -b /tmp/tmpslx8q4hn/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpttohae4a/f1.bed -b /tmp/tmpttohae4a/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpbrox_7nu/f1.bed -b /tmp/tmpbrox_7nu/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpipygl7b5/f1.bed -b /tmp/tmpipygl7b5/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpubzbvqa0/f1.bed -b /tmp/tmpubzbvqa0/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpqcftfka7/f1.bed -b /tmp/tmpqcftfka7/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpd5_rru3i/f1.bed -b /tmp/tmpd5_rru3i/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpzrcslf38/f1.bed -b /tmp/tmpzrcslf38/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp37q_q6r_/f1.bed -b /tmp/tmp37q_q6r_/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpe55xh3ys/f1.bed -b /tmp/tmpe55xh3ys/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpzqttdchd/f1.bed -b /tmp/tmpzqttdchd/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmps7birtov/f1.bed -b /tmp/tmps7birtov/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp66nfcjrp/f1.bed -b /tmp/tmp66nfcjrp/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpn92eaziz/f1.bed -b /tmp/tmpn92eaziz/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpva0mgx44/f1.bed -b /tmp/tmpva0mgx44/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpf376bawk/f1.bed -b /tmp/tmpf376bawk/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpcbry714d/f1.bed -b /tmp/tmpcbry714d/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp_ehv4v77/f1.bed -b /tmp/tmp_ehv4v77/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp5bne_bmp/f1.bed -b /tmp/tmp5bne_bmp/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp7qzx7cqv/f1.bed -b /tmp/tmp7qzx7cqv/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpy4dya8m4/f1.bed -b /tmp/tmpy4dya8m4/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp1hq10k37/f1.bed -b /tmp/tmp1hq10k37/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpywb456wh/f1.bed -b /tmp/tmpywb456wh/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpxtltmzkw/f1.bed -b /tmp/tmpxtltmzkw/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpi3vt914b/f1.bed -b /tmp/tmpi3vt914b/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp3whbi20z/f1.bed -b /tmp/tmp3whbi20z/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpw02nopgm/f1.bed -b /tmp/tmpw02nopgm/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp752hhcbj/f1.bed -b /tmp/tmp752hhcbj/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpf8f2jnio/f1.bed -b /tmp/tmpf8f2jnio/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpehn96vi9/f1.bed -b /tmp/tmpehn96vi9/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpdyppd3k4/f1.bed -b /tmp/tmpdyppd3k4/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp46ch1p6r/f1.bed -b /tmp/tmp46ch1p6r/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpz6gzv7sy/f1.bed -b /tmp/tmpz6gzv7sy/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpo8fiq9bg/f1.bed -b /tmp/tmpo8fiq9bg/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpyl1uqw89/f1.bed -b /tmp/tmpyl1uqw89/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpjzz7cr1g/f1.bed -b /tmp/tmpjzz7cr1g/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpmu9qvvlx/f1.bed -b /tmp/tmpmu9qvvlx/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmprj7_7v38/f1.bed -b /tmp/tmprj7_7v38/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpo6iuro4i/f1.bed -b /tmp/tmpo6iuro4i/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpbpci7aen/f1.bed -b /tmp/tmpbpci7aen/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpnjem8_lx/f1.bed -b /tmp/tmpnjem8_lx/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp6_hjewoq/f1.bed -b /tmp/tmp6_hjewoq/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpooe2sq36/f1.bed -b /tmp/tmpooe2sq36/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpgfu_we0p/f1.bed -b /tmp/tmpgfu_we0p/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp7hy1njvq/f1.bed -b /tmp/tmp7hy1njvq/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmps82kq2mt/f1.bed -b /tmp/tmps82kq2mt/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp3rxrvvty/f1.bed -b /tmp/tmp3rxrvvty/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpw9eakr30/f1.bed -b /tmp/tmpw9eakr30/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp1g6axk7u/f1.bed -b /tmp/tmp1g6axk7u/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp6fvnyu6o/f1.bed -b /tmp/tmp6fvnyu6o/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmprywft1df/f1.bed -b /tmp/tmprywft1df/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpn2lhg27p/f1.bed -b /tmp/tmpn2lhg27p/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpp26rg08o/f1.bed -b /tmp/tmpp26rg08o/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpn5t34cjw/f1.bed -b /tmp/tmpn5t34cjw/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpz_c301pg/f1.bed -b /tmp/tmpz_c301pg/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpxtyv4g2m/f1.bed -b /tmp/tmpxtyv4g2m/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmprgqk6saa/f1.bed -b /tmp/tmprgqk6saa/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp6t8dulg_/f1.bed -b /tmp/tmp6t8dulg_/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp7nm82onn/f1.bed -b /tmp/tmp7nm82onn/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp_sxg5f90/f1.bed -b /tmp/tmp_sxg5f90/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp0l9tw1kd/f1.bed -b /tmp/tmp0l9tw1kd/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmphud30xko/f1.bed -b /tmp/tmphud30xko/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpaivbfvt9/f1.bed -b /tmp/tmpaivbfvt9/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp5m4iliv7/f1.bed -b /tmp/tmp5m4iliv7/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpwsw8sj3a/f1.bed -b /tmp/tmpwsw8sj3a/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp_lgin2_d/f1.bed -b /tmp/tmp_lgin2_d/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpckgj5b4i/f1.bed -b /tmp/tmpckgj5b4i/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpq3ltz5lu/f1.bed -b /tmp/tmpq3ltz5lu/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpx73sp_ii/f1.bed -b /tmp/tmpx73sp_ii/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpaqqv3wfn/f1.bed -b /tmp/tmpaqqv3wfn/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp7l446rab/f1.bed -b /tmp/tmp7l446rab/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpce5okw54/f1.bed -b /tmp/tmpce5okw54/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp_3ei0eh7/f1.bed -b /tmp/tmp_3ei0eh7/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp9blb6qri/f1.bed -b /tmp/tmp9blb6qri/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpo9ncwpfj/f1.bed -b /tmp/tmpo9ncwpfj/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp0y1qcbmt/f1.bed -b /tmp/tmp0y1qcbmt/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpwjv5mlk6/f1.bed -b /tmp/tmpwjv5mlk6/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpe76uu1j_/f1.bed -b /tmp/tmpe76uu1j_/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpsnxo_v3y/f1.bed -b /tmp/tmpsnxo_v3y/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp5kuv_few/f1.bed -b /tmp/tmp5kuv_few/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpfx2jhpau/f1.bed -b /tmp/tmpfx2jhpau/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp6zkqa2_k/f1.bed -b /tmp/tmp6zkqa2_k/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpgqzyfwts/f1.bed -b /tmp/tmpgqzyfwts/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp7jla9d6n/f1.bed -b /tmp/tmp7jla9d6n/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmph2rumaex/f1.bed -b /tmp/tmph2rumaex/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpk4v9w9wz/f1.bed -b /tmp/tmpk4v9w9wz/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpt8wnj48j/f1.bed -b /tmp/tmpt8wnj48j/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpt6slwxrf/f1.bed -b /tmp/tmpt6slwxrf/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmppu9hro1o/f1.bed -b /tmp/tmppu9hro1o/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpafecs9y_/f1.bed -b /tmp/tmpafecs9y_/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpsow55k5z/f1.bed -b /tmp/tmpsow55k5z/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpwx5eacgi/f1.bed -b /tmp/tmpwx5eacgi/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpzd13_qhq/f1.bed -b /tmp/tmpzd13_qhq/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp4b0vypqj/f1.bed -b /tmp/tmp4b0vypqj/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpp8o4gy65/f1.bed -b /tmp/tmpp8o4gy65/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp90_sqkp8/f1.bed -b /tmp/tmp90_sqkp8/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpe4x0xfs4/f1.bed -b /tmp/tmpe4x0xfs4/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpjw1yiocg/f1.bed -b /tmp/tmpjw1yiocg/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpsijj6cgo/f1.bed -b /tmp/tmpsijj6cgo/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpy_j4qebt/f1.bed -b /tmp/tmpy_j4qebt/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpjjl1yz3a/f1.bed -b /tmp/tmpjjl1yz3a/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpk6_s_gz1/f1.bed -b /tmp/tmpk6_s_gz1/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpw9o3sftv/f1.bed -b /tmp/tmpw9o3sftv/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpsam1e4hj/f1.bed -b /tmp/tmpsam1e4hj/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmprg4bp5fc/f1.bed -b /tmp/tmprg4bp5fc/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpttfdsd_m/f1.bed -b /tmp/tmpttfdsd_m/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpshw2t1_p/f1.bed -b /tmp/tmpshw2t1_p/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpnpt4w15c/f1.bed -b /tmp/tmpnpt4w15c/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp89mrz5q0/f1.bed -b /tmp/tmp89mrz5q0/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpu2jobwt1/f1.bed -b /tmp/tmpu2jobwt1/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpm015ztt6/f1.bed -b /tmp/tmpm015ztt6/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpx4n3i2nv/f1.bed -b /tmp/tmpx4n3i2nv/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpolp8rhg2/f1.bed -b /tmp/tmpolp8rhg2/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpuvy0lhr7/f1.bed -b /tmp/tmpuvy0lhr7/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpa9_gmcxn/f1.bed -b /tmp/tmpa9_gmcxn/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp3wcrjscq/f1.bed -b /tmp/tmp3wcrjscq/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpuxawzsvi/f1.bed -b /tmp/tmpuxawzsvi/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpjsz5pzvj/f1.bed -b /tmp/tmpjsz5pzvj/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpy0i639fe/f1.bed -b /tmp/tmpy0i639fe/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpfhpvk0y6/f1.bed -b /tmp/tmpfhpvk0y6/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpo1gtaowd/f1.bed -b /tmp/tmpo1gtaowd/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp4cqqgcjm/f1.bed -b /tmp/tmp4cqqgcjm/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpixo8ai_r/f1.bed -b /tmp/tmpixo8ai_r/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpr9vyl_hc/f1.bed -b /tmp/tmpr9vyl_hc/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpozwnw677/f1.bed -b /tmp/tmpozwnw677/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp5vryle66/f1.bed -b /tmp/tmp5vryle66/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp0zfdhbka/f1.bed -b /tmp/tmp0zfdhbka/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp77_agm6s/f1.bed -b /tmp/tmp77_agm6s/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpbjhme4_o/f1.bed -b /tmp/tmpbjhme4_o/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp82huw6zf/f1.bed -b /tmp/tmp82huw6zf/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpe8s56zxz/f1.bed -b /tmp/tmpe8s56zxz/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpcl4x1yth/f1.bed -b /tmp/tmpcl4x1yth/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpft5n2aa6/f1.bed -b /tmp/tmpft5n2aa6/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpw5f05fbp/f1.bed -b /tmp/tmpw5f05fbp/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpfzcnfsbs/f1.bed -b /tmp/tmpfzcnfsbs/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpeyi4prlh/f1.bed -b /tmp/tmpeyi4prlh/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp4reb00wj/f1.bed -b /tmp/tmp4reb00wj/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp0f_a747r/f1.bed -b /tmp/tmp0f_a747r/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp92_q8rrr/f1.bed -b /tmp/tmp92_q8rrr/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmptmi3h3h3/f1.bed -b /tmp/tmptmi3h3h3/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpv0qz1_gm/f1.bed -b /tmp/tmpv0qz1_gm/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpwm9v4ed_/f1.bed -b /tmp/tmpwm9v4ed_/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpx9ru4ell/f1.bed -b /tmp/tmpx9ru4ell/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp2urgie40/f1.bed -b /tmp/tmp2urgie40/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpd0_le036/f1.bed -b /tmp/tmpd0_le036/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpeq2c0uqw/f1.bed -b /tmp/tmpeq2c0uqw/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp0mdooevc/f1.bed -b /tmp/tmp0mdooevc/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp0cskuz50/f1.bed -b /tmp/tmp0cskuz50/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmprt8nta3a/f1.bed -b /tmp/tmprt8nta3a/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp7hobo14s/f1.bed -b /tmp/tmp7hobo14s/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp6_pqwps4/f1.bed -b /tmp/tmp6_pqwps4/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp257c0z51/f1.bed -b /tmp/tmp257c0z51/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpdvhnefqj/f1.bed -b /tmp/tmpdvhnefqj/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp8plbf5a7/f1.bed -b /tmp/tmp8plbf5a7/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpzjg2plg4/f1.bed -b /tmp/tmpzjg2plg4/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpw8r92usp/f1.bed -b /tmp/tmpw8r92usp/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmptlbe5j2l/f1.bed -b /tmp/tmptlbe5j2l/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp9nr3qiww/f1.bed -b /tmp/tmp9nr3qiww/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpgontwyrd/f1.bed -b /tmp/tmpgontwyrd/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpy5jg1d25/f1.bed -b /tmp/tmpy5jg1d25/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting ___________ test_three_in_a_row[strandedness_chain11-method_chain11] ___________ [gw7] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', False) method_chain = ('set_intersect', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('set_intersect', 'intersect'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E (and 65 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2CMMl21k1u2n5GRAQsAAEXCAq0=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ____________________________ test_set_union[False] _____________________________ [gw0] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness = False @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness", no_opposite) tests/test_binary.py:134: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:149: in test_set_union result = gr.set_union(gr2, strandedness=strandedness) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_set_union( E strandedness=False, E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., # or any other generated value E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., # or any other generated value E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2TABIxYxAAAZAAD') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd cat /tmp/tmphxwydg02/f1.bed /tmp/tmphxwydg02/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpi2kl9433/f1.bed /tmp/tmpi2kl9433/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpgbvzm2ei/f1.bed /tmp/tmpgbvzm2ei/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpesfk3ght/f1.bed /tmp/tmpesfk3ght/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmph1w4vyc2/f1.bed /tmp/tmph1w4vyc2/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpy0g8d43j/f1.bed /tmp/tmpy0g8d43j/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpdhb8l_tj/f1.bed /tmp/tmpdhb8l_tj/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpmoqgfa3p/f1.bed /tmp/tmpmoqgfa3p/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp_rxwcdd4/f1.bed /tmp/tmp_rxwcdd4/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpwa7ipshl/f1.bed /tmp/tmpwa7ipshl/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp1vhmb803/f1.bed /tmp/tmp1vhmb803/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp7e_27cn_/f1.bed /tmp/tmp7e_27cn_/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp3h_l2mto/f1.bed /tmp/tmp3h_l2mto/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpulanyi39/f1.bed /tmp/tmpulanyi39/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpngueggrq/f1.bed /tmp/tmpngueggrq/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpsm8aphc0/f1.bed /tmp/tmpsm8aphc0/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmprfcwl9dl/f1.bed /tmp/tmprfcwl9dl/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpl2ltwzd_/f1.bed /tmp/tmpl2ltwzd_/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpt5zgcmqf/f1.bed /tmp/tmpt5zgcmqf/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpov7dklu3/f1.bed /tmp/tmpov7dklu3/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp7egeji1j/f1.bed /tmp/tmp7egeji1j/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpq2juu9or/f1.bed /tmp/tmpq2juu9or/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp9h_0zfjw/f1.bed /tmp/tmp9h_0zfjw/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp88nhtr_l/f1.bed /tmp/tmp88nhtr_l/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmptx4pvih5/f1.bed /tmp/tmptx4pvih5/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpjk596cbv/f1.bed /tmp/tmpjk596cbv/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpij_9tk8b/f1.bed /tmp/tmpij_9tk8b/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpxukjxnx7/f1.bed /tmp/tmpxukjxnx7/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpev4zd4me/f1.bed /tmp/tmpev4zd4me/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp_yjwabpz/f1.bed /tmp/tmp_yjwabpz/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpa6nld73d/f1.bed /tmp/tmpa6nld73d/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpvne7i01x/f1.bed /tmp/tmpvne7i01x/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmps5m7_l55/f1.bed /tmp/tmps5m7_l55/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp4h4frqfy/f1.bed /tmp/tmp4h4frqfy/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmph635fcsc/f1.bed /tmp/tmph635fcsc/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpcp36yh60/f1.bed /tmp/tmpcp36yh60/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpy_q8t664/f1.bed /tmp/tmpy_q8t664/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpkr4513g7/f1.bed /tmp/tmpkr4513g7/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp75hbezeh/f1.bed /tmp/tmp75hbezeh/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp4abw44vu/f1.bed /tmp/tmp4abw44vu/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp7ky50dxy/f1.bed /tmp/tmp7ky50dxy/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmptuqj_kxd/f1.bed /tmp/tmptuqj_kxd/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpd70hifls/f1.bed /tmp/tmpd70hifls/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpl98wpano/f1.bed /tmp/tmpl98wpano/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpl4z483xl/f1.bed /tmp/tmpl4z483xl/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp2h6y55ap/f1.bed /tmp/tmp2h6y55ap/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpw4pgpvl1/f1.bed /tmp/tmpw4pgpvl1/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpf0nq4dro/f1.bed /tmp/tmpf0nq4dro/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp2qidn0ll/f1.bed /tmp/tmp2qidn0ll/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpcv_soyj2/f1.bed /tmp/tmpcv_soyj2/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpaxq6s9gq/f1.bed /tmp/tmpaxq6s9gq/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpntfbmop6/f1.bed /tmp/tmpntfbmop6/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpu08uxo37/f1.bed /tmp/tmpu08uxo37/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpyn4bujea/f1.bed /tmp/tmpyn4bujea/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpck6aslfe/f1.bed /tmp/tmpck6aslfe/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpz5zc1xjt/f1.bed /tmp/tmpz5zc1xjt/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp6l8mwfmn/f1.bed /tmp/tmp6l8mwfmn/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpm9th5tp6/f1.bed /tmp/tmpm9th5tp6/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpaepav60v/f1.bed /tmp/tmpaepav60v/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpx3nb4s_m/f1.bed /tmp/tmpx3nb4s_m/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpk80u3x2_/f1.bed /tmp/tmpk80u3x2_/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp9q9jn4ow/f1.bed /tmp/tmp9q9jn4ow/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpfjqqj7b3/f1.bed /tmp/tmpfjqqj7b3/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpjmxh5jaj/f1.bed /tmp/tmpjmxh5jaj/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpcbwofzvq/f1.bed /tmp/tmpcbwofzvq/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp6nrdz2l8/f1.bed /tmp/tmp6nrdz2l8/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp2340ca8z/f1.bed /tmp/tmp2340ca8z/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpndyu5kbv/f1.bed /tmp/tmpndyu5kbv/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp5854sx4o/f1.bed /tmp/tmp5854sx4o/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpw282vdkn/f1.bed /tmp/tmpw282vdkn/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmppakrcpm5/f1.bed /tmp/tmppakrcpm5/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp91oycctg/f1.bed /tmp/tmp91oycctg/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmphrksfik0/f1.bed /tmp/tmphrksfik0/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp8dyslvzl/f1.bed /tmp/tmp8dyslvzl/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpj8lbp15h/f1.bed /tmp/tmpj8lbp15h/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpp0tysrk5/f1.bed /tmp/tmpp0tysrk5/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpwfbdhhtp/f1.bed /tmp/tmpwfbdhhtp/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp2_tw3veu/f1.bed /tmp/tmp2_tw3veu/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpx_99hvh8/f1.bed /tmp/tmpx_99hvh8/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp3h44iud0/f1.bed /tmp/tmp3h44iud0/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp_go95lek/f1.bed /tmp/tmp_go95lek/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpmvus1ek9/f1.bed /tmp/tmpmvus1ek9/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpxtsxiwjd/f1.bed /tmp/tmpxtsxiwjd/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpk4x6de6j/f1.bed /tmp/tmpk4x6de6j/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpzet5j6bd/f1.bed /tmp/tmpzet5j6bd/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpzmok3zao/f1.bed /tmp/tmpzmok3zao/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpad295g6l/f1.bed /tmp/tmpad295g6l/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpejiu_20y/f1.bed /tmp/tmpejiu_20y/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmptrb2z4yl/f1.bed /tmp/tmptrb2z4yl/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpc3ea5kt5/f1.bed /tmp/tmpc3ea5kt5/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp7w3nl_t8/f1.bed /tmp/tmp7w3nl_t8/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpangoh6kb/f1.bed /tmp/tmpangoh6kb/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpm9dr7z5x/f1.bed /tmp/tmpm9dr7z5x/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpmn_3cayw/f1.bed /tmp/tmpmn_3cayw/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp2qv7ms7o/f1.bed /tmp/tmp2qv7ms7o/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp8nnqo5f4/f1.bed /tmp/tmp8nnqo5f4/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpg80g_fkx/f1.bed /tmp/tmpg80g_fkx/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpcsd2xllx/f1.bed /tmp/tmpcsd2xllx/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmphtndclc4/f1.bed /tmp/tmphtndclc4/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpg4s_dwt3/f1.bed /tmp/tmpg4s_dwt3/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpqjzz0ewa/f1.bed /tmp/tmpqjzz0ewa/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpsbytvawf/f1.bed /tmp/tmpsbytvawf/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpi22sig6x/f1.bed /tmp/tmpi22sig6x/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpgv5gb84b/f1.bed /tmp/tmpgv5gb84b/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpc_6spk3b/f1.bed /tmp/tmpc_6spk3b/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpf730t6yf/f1.bed /tmp/tmpf730t6yf/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpe_nhuwj1/f1.bed /tmp/tmpe_nhuwj1/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpt43ss15r/f1.bed /tmp/tmpt43ss15r/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpdefokuy0/f1.bed /tmp/tmpdefokuy0/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpw7lp5lw2/f1.bed /tmp/tmpw7lp5lw2/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpsfhfpry5/f1.bed /tmp/tmpsfhfpry5/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpu228l0cx/f1.bed /tmp/tmpu228l0cx/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpb68lw1xb/f1.bed /tmp/tmpb68lw1xb/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpabed3lfk/f1.bed /tmp/tmpabed3lfk/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpw8v3ox58/f1.bed /tmp/tmpw8v3ox58/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmph8ync75n/f1.bed /tmp/tmph8ync75n/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpfnds8fo6/f1.bed /tmp/tmpfnds8fo6/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp3ku5edif/f1.bed /tmp/tmp3ku5edif/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmppth5gkxu/f1.bed /tmp/tmppth5gkxu/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp7tty_i5f/f1.bed /tmp/tmp7tty_i5f/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpnz3wuadl/f1.bed /tmp/tmpnz3wuadl/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpwt64dk1u/f1.bed /tmp/tmpwt64dk1u/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpwynkrg3l/f1.bed /tmp/tmpwynkrg3l/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp4tpfadxu/f1.bed /tmp/tmp4tpfadxu/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp2lr5pkoj/f1.bed /tmp/tmp2lr5pkoj/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpzavg_oop/f1.bed /tmp/tmpzavg_oop/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpdcxzv8o3/f1.bed /tmp/tmpdcxzv8o3/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpyqavweeu/f1.bed /tmp/tmpyqavweeu/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpfuqfw8m3/f1.bed /tmp/tmpfuqfw8m3/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpcffkjpjf/f1.bed /tmp/tmpcffkjpjf/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpk0nxz1im/f1.bed /tmp/tmpk0nxz1im/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpev2s44au/f1.bed /tmp/tmpev2s44au/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpd89zhnlu/f1.bed /tmp/tmpd89zhnlu/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpqd_hhlkn/f1.bed /tmp/tmpqd_hhlkn/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpa13f_d1v/f1.bed /tmp/tmpa13f_d1v/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpjtxuw62q/f1.bed /tmp/tmpjtxuw62q/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpwpzbn0f2/f1.bed /tmp/tmpwpzbn0f2/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpbfii7wzr/f1.bed /tmp/tmpbfii7wzr/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpgm1fdqes/f1.bed /tmp/tmpgm1fdqes/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp8do743e6/f1.bed /tmp/tmp8do743e6/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp1olz4b9r/f1.bed /tmp/tmp1olz4b9r/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpvqe1_9yh/f1.bed /tmp/tmpvqe1_9yh/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp2qvs7fil/f1.bed /tmp/tmp2qvs7fil/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpflcglzzp/f1.bed /tmp/tmpflcglzzp/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpsesdfl_b/f1.bed /tmp/tmpsesdfl_b/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpnxbb3mvd/f1.bed /tmp/tmpnxbb3mvd/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpyx0lak89/f1.bed /tmp/tmpyx0lak89/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp1ftssfgs/f1.bed /tmp/tmp1ftssfgs/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp6kc_1xsd/f1.bed /tmp/tmp6kc_1xsd/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpjd8ftqnb/f1.bed /tmp/tmpjd8ftqnb/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpw3tvcp8i/f1.bed /tmp/tmpw3tvcp8i/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpalcvcm93/f1.bed /tmp/tmpalcvcm93/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpgvjoyxjs/f1.bed /tmp/tmpgvjoyxjs/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpgwxi_dyr/f1.bed /tmp/tmpgwxi_dyr/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp2zxggxzl/f1.bed /tmp/tmp2zxggxzl/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp3y2u0xrz/f1.bed /tmp/tmp3y2u0xrz/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp_jix9isc/f1.bed /tmp/tmp_jix9isc/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmplr57yf6v/f1.bed /tmp/tmplr57yf6v/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpu0192d2i/f1.bed /tmp/tmpu0192d2i/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp3bhn4anw/f1.bed /tmp/tmp3bhn4anw/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp0jzdtuny/f1.bed /tmp/tmp0jzdtuny/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpht239c90/f1.bed /tmp/tmpht239c90/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpvtgfucxz/f1.bed /tmp/tmpvtgfucxz/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp4zkg5360/f1.bed /tmp/tmp4zkg5360/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp0djkslit/f1.bed /tmp/tmp0djkslit/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpx3evep_z/f1.bed /tmp/tmpx3evep_z/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpfi9bh7zs/f1.bed /tmp/tmpfi9bh7zs/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpk7uravab/f1.bed /tmp/tmpk7uravab/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp90eu2v4r/f1.bed /tmp/tmp90eu2v4r/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpt23h_x4b/f1.bed /tmp/tmpt23h_x4b/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp60onwdzl/f1.bed /tmp/tmp60onwdzl/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpjpgflip0/f1.bed /tmp/tmpjpgflip0/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpwb2g0stu/f1.bed /tmp/tmpwb2g0stu/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmphy465cru/f1.bed /tmp/tmphy465cru/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpytud76pq/f1.bed /tmp/tmpytud76pq/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpan8gh06b/f1.bed /tmp/tmpan8gh06b/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmphj5hny6j/f1.bed /tmp/tmphj5hny6j/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpbyzi8734/f1.bed /tmp/tmpbyzi8734/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmprmd9vr0l/f1.bed /tmp/tmprmd9vr0l/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpu6jvr_p8/f1.bed /tmp/tmpu6jvr_p8/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp6bmgi2at/f1.bed /tmp/tmp6bmgi2at/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp94dw856u/f1.bed /tmp/tmp94dw856u/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp1rsgnwy8/f1.bed /tmp/tmp1rsgnwy8/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp7_azbock/f1.bed /tmp/tmp7_azbock/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmptaxyx54g/f1.bed /tmp/tmptaxyx54g/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpnixyr0ux/f1.bed /tmp/tmpnixyr0ux/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp_8o5qf33/f1.bed /tmp/tmp_8o5qf33/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmph8e17nhe/f1.bed /tmp/tmph8e17nhe/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp1u8lq5g8/f1.bed /tmp/tmp1u8lq5g8/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpxyyfbike/f1.bed /tmp/tmpxyyfbike/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpj0eg4hpu/f1.bed /tmp/tmpj0eg4hpu/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpsfksco50/f1.bed /tmp/tmpsfksco50/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpt3kjkkdl/f1.bed /tmp/tmpt3kjkkdl/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp5_23lj8d/f1.bed /tmp/tmp5_23lj8d/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp_4kix8e5/f1.bed /tmp/tmp_4kix8e5/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp0irzhiuo/f1.bed /tmp/tmp0irzhiuo/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpwbp6i7mp/f1.bed /tmp/tmpwbp6i7mp/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp7jozbr7k/f1.bed /tmp/tmp7jozbr7k/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpuk6a15_x/f1.bed /tmp/tmpuk6a15_x/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpi6tfpif7/f1.bed /tmp/tmpi6tfpif7/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp92ul2b_m/f1.bed /tmp/tmp92ul2b_m/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp1pn_akvl/f1.bed /tmp/tmp1pn_akvl/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp2b2ua3dv/f1.bed /tmp/tmp2b2ua3dv/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmplbzzb7qy/f1.bed /tmp/tmplbzzb7qy/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp2wjt694a/f1.bed /tmp/tmp2wjt694a/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpyebx1i84/f1.bed /tmp/tmpyebx1i84/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmphvz4uw5s/f1.bed /tmp/tmphvz4uw5s/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp4hm6jc4g/f1.bed /tmp/tmp4hm6jc4g/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpmpc2k21k/f1.bed /tmp/tmpmpc2k21k/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpbl98kw7v/f1.bed /tmp/tmpbl98kw7v/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmps_8ppbf9/f1.bed /tmp/tmps_8ppbf9/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpzjyu4kqn/f1.bed /tmp/tmpzjyu4kqn/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpmepmfpr1/f1.bed /tmp/tmpmepmfpr1/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpfyvfzl_d/f1.bed /tmp/tmpfyvfzl_d/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpqzizcizf/f1.bed /tmp/tmpqzizcizf/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpcrvgfydt/f1.bed /tmp/tmpcrvgfydt/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpu9_3vh5_/f1.bed /tmp/tmpu9_3vh5_/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpn5vwky_c/f1.bed /tmp/tmpn5vwky_c/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpo5i17c9t/f1.bed /tmp/tmpo5i17c9t/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpy2y6jqo7/f1.bed /tmp/tmpy2y6jqo7/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpfxzkryui/f1.bed /tmp/tmpfxzkryui/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp54l63qrx/f1.bed /tmp/tmp54l63qrx/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpbl0k46h8/f1.bed /tmp/tmpbl0k46h8/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpzkag4ajw/f1.bed /tmp/tmpzkag4ajw/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpwt_l9sst/f1.bed /tmp/tmpwt_l9sst/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpo9r6q34d/f1.bed /tmp/tmpo9r6q34d/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpayif_eju/f1.bed /tmp/tmpayif_eju/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpalq_rozu/f1.bed /tmp/tmpalq_rozu/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpum3wdul0/f1.bed /tmp/tmpum3wdul0/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp3ikkqicj/f1.bed /tmp/tmp3ikkqicj/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpgtnect5o/f1.bed /tmp/tmpgtnect5o/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpuhf4sjxs/f1.bed /tmp/tmpuhf4sjxs/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpwn2olx1q/f1.bed /tmp/tmpwn2olx1q/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpumthjm3k/f1.bed /tmp/tmpumthjm3k/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpwdt1xuze/f1.bed /tmp/tmpwdt1xuze/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpr4mhujw5/f1.bed /tmp/tmpr4mhujw5/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpqckjaeis/f1.bed /tmp/tmpqckjaeis/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmptq_3_phz/f1.bed /tmp/tmptq_3_phz/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmput6aby7a/f1.bed /tmp/tmput6aby7a/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpa5jv2jdb/f1.bed /tmp/tmpa5jv2jdb/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmprxiw8i7p/f1.bed /tmp/tmprxiw8i7p/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpprid36ce/f1.bed /tmp/tmpprid36ce/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpb2vgx_xk/f1.bed /tmp/tmpb2vgx_xk/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpa9dm9aax/f1.bed /tmp/tmpa9dm9aax/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp671rbeig/f1.bed /tmp/tmp671rbeig/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpdkqyv99t/f1.bed /tmp/tmpdkqyv99t/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp6zw99yvo/f1.bed /tmp/tmp6zw99yvo/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp418e361q/f1.bed /tmp/tmp418e361q/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpm4h393zf/f1.bed /tmp/tmpm4h393zf/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpdkc0kpgz/f1.bed /tmp/tmpdkc0kpgz/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpc491il06/f1.bed /tmp/tmpc491il06/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmply4gme_q/f1.bed /tmp/tmply4gme_q/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpq7af1j0j/f1.bed /tmp/tmpq7af1j0j/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpbh5l149q/f1.bed /tmp/tmpbh5l149q/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp6__cpfmj/f1.bed /tmp/tmp6__cpfmj/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpl8lp8gz4/f1.bed /tmp/tmpl8lp8gz4/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpmgfq8ivi/f1.bed /tmp/tmpmgfq8ivi/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmprse9zhf_/f1.bed /tmp/tmprse9zhf_/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpw_l84pi_/f1.bed /tmp/tmpw_l84pi_/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp06s1ranc/f1.bed /tmp/tmp06s1ranc/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp8tv9936q/f1.bed /tmp/tmp8tv9936q/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpabu4lc49/f1.bed /tmp/tmpabu4lc49/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp8gu2j0lo/f1.bed /tmp/tmp8gu2j0lo/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmptboj4xyn/f1.bed /tmp/tmptboj4xyn/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp_hy__cw2/f1.bed /tmp/tmp_hy__cw2/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpxdh1yg7v/f1.bed /tmp/tmpxdh1yg7v/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpo836klrd/f1.bed /tmp/tmpo836klrd/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpq3f326jn/f1.bed /tmp/tmpq3f326jn/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpdc_2hrnk/f1.bed /tmp/tmpdc_2hrnk/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp440hfmh9/f1.bed /tmp/tmp440hfmh9/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpaqkj2ii3/f1.bed /tmp/tmpaqkj2ii3/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpox1dsy08/f1.bed /tmp/tmpox1dsy08/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp3w4a2fyd/f1.bed /tmp/tmp3w4a2fyd/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmprwnt4wa3/f1.bed /tmp/tmprwnt4wa3/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpery_6bdb/f1.bed /tmp/tmpery_6bdb/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpb57pfv4c/f1.bed /tmp/tmpb57pfv4c/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp844yk1hz/f1.bed /tmp/tmp844yk1hz/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp6c99y7th/f1.bed /tmp/tmp6c99y7th/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpcncjfz6u/f1.bed /tmp/tmpcncjfz6u/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp67rw36or/f1.bed /tmp/tmp67rw36or/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp_dsbj1zq/f1.bed /tmp/tmp_dsbj1zq/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpwj4cpekq/f1.bed /tmp/tmpwj4cpekq/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpocqk8wif/f1.bed /tmp/tmpocqk8wif/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp88bdeiaz/f1.bed /tmp/tmp88bdeiaz/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp8nqu3azb/f1.bed /tmp/tmp8nqu3azb/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpbybbien_/f1.bed /tmp/tmpbybbien_/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpdjfkqnfp/f1.bed /tmp/tmpdjfkqnfp/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpm_4vumu5/f1.bed /tmp/tmpm_4vumu5/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpo2k_s8ew/f1.bed /tmp/tmpo2k_s8ew/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpqd1ej7id/f1.bed /tmp/tmpqd1ej7id/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpfohspoev/f1.bed /tmp/tmpfohspoev/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpqdikp40l/f1.bed /tmp/tmpqdikp40l/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpxzv2ti9u/f1.bed /tmp/tmpxzv2ti9u/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpyn6pfczu/f1.bed /tmp/tmpyn6pfczu/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpo22cbvse/f1.bed /tmp/tmpo22cbvse/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpfmh6_5p0/f1.bed /tmp/tmpfmh6_5p0/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpgwli_bc1/f1.bed /tmp/tmpgwli_bc1/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpuvc4ncit/f1.bed /tmp/tmpuvc4ncit/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpws1o_dqy/f1.bed /tmp/tmpws1o_dqy/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpxouid18c/f1.bed /tmp/tmpxouid18c/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpcikjoovw/f1.bed /tmp/tmpcikjoovw/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpjqlglaiv/f1.bed /tmp/tmpjqlglaiv/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpn5q6wv4p/f1.bed /tmp/tmpn5q6wv4p/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpj6pu7xqy/f1.bed /tmp/tmpj6pu7xqy/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpm0hfpw6i/f1.bed /tmp/tmpm0hfpw6i/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpvpmqwv16/f1.bed /tmp/tmpvpmqwv16/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpcbwjspju/f1.bed /tmp/tmpcbwjspju/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpctx1_449/f1.bed /tmp/tmpctx1_449/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpj_y0ccox/f1.bed /tmp/tmpj_y0ccox/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmptu3ut2xi/f1.bed /tmp/tmptu3ut2xi/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpnu32p0mb/f1.bed /tmp/tmpnu32p0mb/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpqu9ek9u7/f1.bed /tmp/tmpqu9ek9u7/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp17cy40v5/f1.bed /tmp/tmp17cy40v5/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp0u_i_jn2/f1.bed /tmp/tmp0u_i_jn2/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpnnjioypk/f1.bed /tmp/tmpnnjioypk/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpn61lapve/f1.bed /tmp/tmpn61lapve/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpy1c7pzp_/f1.bed /tmp/tmpy1c7pzp_/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp3x8_jjez/f1.bed /tmp/tmp3x8_jjez/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpbiup9v5r/f1.bed /tmp/tmpbiup9v5r/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpbc0xxo92/f1.bed /tmp/tmpbc0xxo92/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp1eqqnm74/f1.bed /tmp/tmp1eqqnm74/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpzei14fiy/f1.bed /tmp/tmpzei14fiy/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpo0h6a2sq/f1.bed /tmp/tmpo0h6a2sq/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpas06ek21/f1.bed /tmp/tmpas06ek21/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpnvn09crc/f1.bed /tmp/tmpnvn09crc/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpel8mbpky/f1.bed /tmp/tmpel8mbpky/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp_tkksvqv/f1.bed /tmp/tmp_tkksvqv/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp2ysjpaow/f1.bed /tmp/tmp2ysjpaow/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp49h6koi7/f1.bed /tmp/tmp49h6koi7/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpgv6ma3br/f1.bed /tmp/tmpgv6ma3br/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpfj41x6te/f1.bed /tmp/tmpfj41x6te/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpru7uu_xp/f1.bed /tmp/tmpru7uu_xp/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpqj_f6eom/f1.bed /tmp/tmpqj_f6eom/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp66xjbl8e/f1.bed /tmp/tmp66xjbl8e/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpqqfr2sk5/f1.bed /tmp/tmpqqfr2sk5/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp_f0q73xv/f1.bed /tmp/tmp_f0q73xv/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpvi4ar4yq/f1.bed /tmp/tmpvi4ar4yq/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmprfeed7jr/f1.bed /tmp/tmprfeed7jr/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpz4t_ohwz/f1.bed /tmp/tmpz4t_ohwz/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp_0ltsa20/f1.bed /tmp/tmp_0ltsa20/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp0yz9u37y/f1.bed /tmp/tmp0yz9u37y/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmps1dl9lu3/f1.bed /tmp/tmps1dl9lu3/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpgk4m61my/f1.bed /tmp/tmpgk4m61my/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpihnfxpuh/f1.bed /tmp/tmpihnfxpuh/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpbimqryyg/f1.bed /tmp/tmpbimqryyg/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp5ukw7lz4/f1.bed /tmp/tmp5ukw7lz4/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp4ogdgd1v/f1.bed /tmp/tmp4ogdgd1v/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmps9w72v9w/f1.bed /tmp/tmps9w72v9w/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpparcn5tv/f1.bed /tmp/tmpparcn5tv/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp0shnnc_5/f1.bed /tmp/tmp0shnnc_5/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpgtoqd9p6/f1.bed /tmp/tmpgtoqd9p6/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpvoxljuaa/f1.bed /tmp/tmpvoxljuaa/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpzb5qedd7/f1.bed /tmp/tmpzb5qedd7/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpehjihli5/f1.bed /tmp/tmpehjihli5/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain60-method_chain60] ___________ [gw9] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', 'same') method_chain = ('set_intersect', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('set_intersect', 'intersect'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E /usr/lib/python3/dist-packages/natsort/utils.py:344 E (and 66 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2CAA0YGLAAAADUAAg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ____________________ test_nearest[upstream-False-opposite] _____________________ [gw2] linux -- Python 3.12.6 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 880, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 323, in test_nearest | @pytest.mark.parametrize("nearest_how,overlap,strandedness", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1722, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 351, in test_nearest | result = gr.nearest( | ^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 118, in _nearest | r_idx, dist = _previous_nonoverlapping(df_to_find_nearest_in.Start, | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_nearest( | nearest_how='upstream', | overlap=False, | strandedness='opposite', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | (and 103 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2TABIxYhAAAZQAE') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 351, in test_nearest | result = gr.nearest( | ^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 115, in _nearest | r_idx, dist = _next_nonoverlapping(df_to_find_nearest_in.End, | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 62, in _next_nonoverlapping | r_idx, dist = nearest_next_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 34, in sorted_nearest.src.sorted_nearest.nearest_next_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_nearest( | nearest_how='upstream', | overlap=False, | strandedness='opposite', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | (and 103 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2TAAIyMUBpJDAAAgQAF') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpd9lra53j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd9lra53j/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpv8erk52k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv8erk52k/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpszwdb71f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpszwdb71f/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppgrbxgrk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppgrbxgrk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdhag_4nf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdhag_4nf/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpk13hrmev/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk13hrmev/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9_1tj_xb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9_1tj_xb/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcx8dw3bt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcx8dw3bt/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7ksy57sm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7ksy57sm/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpizyq7zwp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpizyq7zwp/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpo1x0tahr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo1x0tahr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgcx_71r3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgcx_71r3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpx3752m5o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx3752m5o/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpj48y3cap/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj48y3cap/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9jsjnr5z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9jsjnr5z/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnw3v9kfx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnw3v9kfx/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4ex_6v3i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4ex_6v3i/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpim_w7rth/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpim_w7rth/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptidy4kdx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptidy4kdx/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpf3yqw5c2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf3yqw5c2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplnhgbbyb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplnhgbbyb/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpl7ab7ooi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl7ab7ooi/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjm7pj6iv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjm7pj6iv/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsack0b98/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsack0b98/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzutjytvw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzutjytvw/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpb3d0uvya/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb3d0uvya/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmlugwqkm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmlugwqkm/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpglojatvo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpglojatvo/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4hntbl9w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4hntbl9w/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpik7qynak/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpik7qynak/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp05_0p5h_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp05_0p5h_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4mbdagri/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4mbdagri/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpk0nmxb75/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk0nmxb75/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5xxmp7_f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5xxmp7_f/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpc5kwme7d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc5kwme7d/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgv7m6nnz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgv7m6nnz/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphzkksvtk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphzkksvtk/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphatx59k9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphatx59k9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsx2amyo0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsx2amyo0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpiikf79m0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiikf79m0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpv81yqwq0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv81yqwq0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphlbhbrmd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphlbhbrmd/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9mxsbbcg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9mxsbbcg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6plw5ryt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6plw5ryt/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbgoebo2a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbgoebo2a/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6h_7_1yw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6h_7_1yw/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpssg4uses/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpssg4uses/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplh_m_jp4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplh_m_jp4/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpg7cdg_dg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg7cdg_dg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpedoj94t1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpedoj94t1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvewvv_aq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvewvv_aq/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp74m52ymz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp74m52ymz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpaf550_oc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaf550_oc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppmt1sjf3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppmt1sjf3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwdzeip5g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwdzeip5g/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_68nyl3q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_68nyl3q/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4xd9b2sc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4xd9b2sc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdknnsrrn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdknnsrrn/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4zqt81y1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4zqt81y1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpw2fulg51/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw2fulg51/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpl4wcgm9k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl4wcgm9k/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpc5ok7oy8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc5ok7oy8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpo7oqag6q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo7oqag6q/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsffojtzh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsffojtzh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkbwvzkp6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkbwvzkp6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqh05ziui/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqh05ziui/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpy3ib2iy5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy3ib2iy5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppay2orzy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppay2orzy/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgdvpa8s8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgdvpa8s8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprkt0ukb6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprkt0ukb6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9arau53m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9arau53m/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsfodop38/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsfodop38/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjwfd6mz6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjwfd6mz6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpho0l6ofv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpho0l6ofv/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8uwgci3r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8uwgci3r/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpa_8glgid/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa_8glgid/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphwlg6vwt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphwlg6vwt/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp16uaea4v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp16uaea4v/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpetkwc_i4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpetkwc_i4/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp18vqn6vq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp18vqn6vq/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdyyqzu6d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdyyqzu6d/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpd71a_8_x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd71a_8_x/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpewd8n7ct/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpewd8n7ct/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmwjb3vpb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmwjb3vpb/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0esrbnj9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0esrbnj9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpr7lzlxdb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr7lzlxdb/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpa079rsfa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa079rsfa/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpp287e1dk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp287e1dk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvuzt30oo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvuzt30oo/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpw77hp_re/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw77hp_re/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpm3028jzx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm3028jzx/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpo07c47ff/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo07c47ff/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp18ehwx4i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp18ehwx4i/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsf04i_no/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsf04i_no/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpar8axofr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpar8axofr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3ld9v24d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3ld9v24d/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjim9xsoc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjim9xsoc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqwrk0ln8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqwrk0ln8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpg4rbi1hk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg4rbi1hk/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqhzdn5_c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqhzdn5_c/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp67cevosj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp67cevosj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcjfbxx80/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcjfbxx80/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphkxy05z1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphkxy05z1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpar6cuq0o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpar6cuq0o/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpybrymlk4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpybrymlk4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe25gtgs_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe25gtgs_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuhmr4_bk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuhmr4_bk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpep_om1_m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpep_om1_m/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6l38dqlj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6l38dqlj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqbg_zdjg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqbg_zdjg/f2.bed) ____________ test_three_in_a_row[strandedness_chain4-method_chain4] ____________ [gw5] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', False), method_chain = ('set_union', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('set_union', 'intersect'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E (and 179 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BU9l9iLsTmxsjIgAUAACyBAa8=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ___________________ test_k_nearest[None-True-opposite-last] ____________________ [gw4] linux -- Python 3.12.6 /usr/bin/python3.12 nearest_how = None, overlap = True, strandedness = 'opposite', ties = 'last' @pytest.mark.bedtools > @pytest.mark.explore tests/test_binary.py:510: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:548: in test_k_nearest result = gr.k_nearest( pyranges/pyranges.py:2450: in k_nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/k_nearest.py:180: in _nearest df = __nearest(d1, d2, **kwargs) pyranges/methods/k_nearest.py:71: in nearest plidx, pridx, pdist = nearest_previous_idx(d1, d2, d1.__k__.values, ties) pyranges/methods/k_nearest.py:28: in nearest_previous_idx lidx, ridx_pos, dist = k_nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_k_nearest( E nearest_how=None, E overlap=True, E strandedness='opposite', E ties='last', E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:14 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:15 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:160 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:19 E (and 39 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2QAA0YGBGDEEGIEAACLAAY=') as a decorator on your test case sorted_nearest/src/k_nearest.pyx:28: ValueError ----------------------------- Captured stdout call ----------------------------- ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkshvk0fy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkshvk0fy/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpo39l369y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo39l369y/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpn8lyhx8a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn8lyhx8a/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9q610v3p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9q610v3p/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpl0qd_u4h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl0qd_u4h/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2ro4ddl2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2ro4ddl2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmprge42mu3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprge42mu3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsfbftyyw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsfbftyyw/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmprdouxtrt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprdouxtrt/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpik_o66df/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpik_o66df/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnu9mmxjx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnu9mmxjx/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7d4av7ig/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7d4av7ig/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpecxsu5zq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpecxsu5zq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp12xze00y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp12xze00y/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbd46ype4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbd46ype4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpacsgkie_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpacsgkie_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpe46wcybn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe46wcybn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp33ds9om0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp33ds9om0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpoud8kqgr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoud8kqgr/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpt_ipt12y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt_ipt12y/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpq7lv3ufa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq7lv3ufa/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmplvz4r6bi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplvz4r6bi/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpthn8bvny/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpthn8bvny/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpu_ckr9fi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu_ckr9fi/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp64zhy5kj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp64zhy5kj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2o9nik9j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2o9nik9j/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmps0dooyb9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps0dooyb9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwaghrxdi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwaghrxdi/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmppjm9gpf7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppjm9gpf7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpft1k4y25/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpft1k4y25/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4n1sauf3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4n1sauf3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpd21uz5ul/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd21uz5ul/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpp7zvgmgh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp7zvgmgh/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpklu7l9km/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpklu7l9km/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpr37vjirz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr37vjirz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmppax205u6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppax205u6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxxmda6h9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxxmda6h9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7c3dep9r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7c3dep9r/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpewrgk0l_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpewrgk0l_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyf5iwhpf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyf5iwhpf/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgki46p8t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgki46p8t/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpf848c9sr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf848c9sr/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpttgir6pd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpttgir6pd/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqd6486nw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqd6486nw/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4fy5u3mv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4fy5u3mv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1h5ix52o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1h5ix52o/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsxn5z7sl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsxn5z7sl/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqn08a6jz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqn08a6jz/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpws7ggwz6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpws7ggwz6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp16e_l931/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp16e_l931/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpj3f_3k1t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj3f_3k1t/f2.bed) ----------------------------- Captured stderr call ----------------------------- Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr15 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr15 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr15 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr15 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr15 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr15 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr15 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. _____________________ test_k_nearest[None-True-same-last] ______________________ [gw4] linux -- Python 3.12.6 /usr/bin/python3.12 nearest_how = None, overlap = True, strandedness = 'same', ties = 'last' @pytest.mark.bedtools > @pytest.mark.explore tests/test_binary.py:510: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:548: in test_k_nearest result = gr.k_nearest( pyranges/pyranges.py:2450: in k_nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/k_nearest.py:180: in _nearest df = __nearest(d1, d2, **kwargs) pyranges/methods/k_nearest.py:71: in nearest plidx, pridx, pdist = nearest_previous_idx(d1, d2, d1.__k__.values, ties) pyranges/methods/k_nearest.py:28: in nearest_previous_idx lidx, ridx_pos, dist = k_nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_k_nearest( E nearest_how=None, E overlap=True, E strandedness='same', E ties='last', E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:14 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:15 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:160 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:19 E (and 38 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2TABIxYxAAAZAAD') as a decorator on your test case sorted_nearest/src/k_nearest.pyx:28: ValueError ----------------------------- Captured stdout call ----------------------------- ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2ng59uq5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2ng59uq5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpy5g63c9k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy5g63c9k/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1p8e7e08/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1p8e7e08/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmptfxermpm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptfxermpm/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmprtckw2ju/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprtckw2ju/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpf77sccjh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf77sccjh/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdaz9_jvl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdaz9_jvl/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_60too_a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_60too_a/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjr35rnel/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjr35rnel/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp70fmf2ef/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp70fmf2ef/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpul_29f7q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpul_29f7q/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9dwr5sel/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9dwr5sel/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpovdyqcwc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpovdyqcwc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmptw84o0yo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptw84o0yo/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpy489d517/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy489d517/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1jpx_u01/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1jpx_u01/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpiv2jge3g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiv2jge3g/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpy5kzmet8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy5kzmet8/f2.bed) ----------------------------- Captured stderr call ----------------------------- Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. ___________ test_three_in_a_row[strandedness_chain49-method_chain49] ___________ [gw10] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', 'same'), method_chain = ('set_union', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('set_union', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E (and 231 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2Dka9vazC34koGBkQETAABIjgLU') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ___________ test_three_in_a_row[strandedness_chain36-method_chain36] ___________ [gw8] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', False) method_chain = ('subtract', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('subtract', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:112 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:117 E (and 119 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2C0S+jeUsfAyMjAyIAJAD9DAmA=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') _____________________ test_k_nearest[None-True-False-last] _____________________ [gw4] linux -- Python 3.12.6 /usr/bin/python3.12 nearest_how = None, overlap = True, strandedness = False, ties = 'last' @pytest.mark.bedtools > @pytest.mark.explore tests/test_binary.py:510: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:548: in test_k_nearest result = gr.k_nearest( pyranges/pyranges.py:2450: in k_nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:292: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/k_nearest.py:180: in _nearest df = __nearest(d1, d2, **kwargs) pyranges/methods/k_nearest.py:71: in nearest plidx, pridx, pdist = nearest_previous_idx(d1, d2, d1.__k__.values, ties) pyranges/methods/k_nearest.py:28: in nearest_previous_idx lidx, ridx_pos, dist = k_nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_k_nearest( E nearest_how=None, E overlap=True, E strandedness=False, E ties='last', E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:14 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:15 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:160 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:19 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:28 E (and 37 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2TABIxYxAAAZAAD') as a decorator on your test case sorted_nearest/src/k_nearest.pyx:28: ValueError ----------------------------- Captured stdout call ----------------------------- ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8gw_3od5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8gw_3od5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9up2gqb_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9up2gqb_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_1ovjnqi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_1ovjnqi/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnrdxcbil/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnrdxcbil/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmppx8_wi4m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppx8_wi4m/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9ma39z8l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9ma39z8l/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6oj_eklv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6oj_eklv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdkyfeyij/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdkyfeyij/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpv1dse14s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv1dse14s/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5qyads5l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5qyads5l/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpn1bqnxou/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn1bqnxou/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpq2ly4xks/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq2ly4xks/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpe9re5n4y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe9re5n4y/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpci_5_4bo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpci_5_4bo/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7soexxy5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7soexxy5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2r7v2lg7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2r7v2lg7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpt4epzd3j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt4epzd3j/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpq89jnkq0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq89jnkq0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmptw5g90wl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptw5g90wl/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsu0xivct/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsu0xivct/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpijh1tj6d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpijh1tj6d/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0rra6ie6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0rra6ie6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjq6m5p5a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjq6m5p5a/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpk0_a6_o2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk0_a6_o2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7vsujef6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7vsujef6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmplh_rvcg_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplh_rvcg_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4z_iafuw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4z_iafuw/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4dvsfyuk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4dvsfyuk/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpf2igpeh8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf2igpeh8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpq1ifv8js/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq1ifv8js/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwj9j2og8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwj9j2og8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5h5nyxaf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5h5nyxaf/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkifsmsn5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkifsmsn5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp84k1_avq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp84k1_avq/f2.bed) ----------------------------- Captured stderr call ----------------------------- Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrM than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrM than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr15 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr10 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. _________________________ test_k_nearest_1_vs_nearest __________________________ [gw4] linux -- Python 3.12.6 /usr/bin/python3.12 @settings( > max_examples=max_examples, deadline=deadline, print_blob=True, suppress_health_check=HealthCheck.all()) tests/test_binary.py:576: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:583: in test_k_nearest_1_vs_nearest result_k = gr.k_nearest(gr2, k=1, strandedness=None, overlap=True, how=None) pyranges/pyranges.py:2450: in k_nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:292: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/k_nearest.py:180: in _nearest df = __nearest(d1, d2, **kwargs) pyranges/methods/k_nearest.py:71: in nearest plidx, pridx, pdist = nearest_previous_idx(d1, d2, d1.__k__.values, ties) pyranges/methods/k_nearest.py:28: in nearest_previous_idx lidx, ridx_pos, dist = k_nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_k_nearest_1_vs_nearest( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:14 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:15 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:160 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:19 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:28 E (and 37 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2TABIxYxAAAZAAD') as a decorator on your test case sorted_nearest/src/k_nearest.pyx:24: ValueError ___________ test_three_in_a_row[strandedness_chain12-method_chain12] ___________ [gw7] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', False) method_chain = ('set_intersect', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('set_intersect', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:140 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E (and 106 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2AUVP51zEk0m5GBkQETAABGqQK6') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') 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('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 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'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') _____________________ test_nearest[downstream-True-False] ______________________ [gw2] linux -- Python 3.12.6 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 880, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 323, in test_nearest | @pytest.mark.parametrize("nearest_how,overlap,strandedness", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1722, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 3 distinct failures. (3 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 351, in test_nearest | result = gr.nearest( | ^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 292, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 118, in _nearest | r_idx, dist = _previous_nonoverlapping(df_to_find_nearest_in.Start, | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_nearest( | nearest_how='downstream', | overlap=True, | strandedness=False, | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:11 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:12 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:101 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 | (and 70 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2TAAIyMUBpOMDAAAACIAAY=') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 351, in test_nearest | result = gr.nearest( | ^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 292, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 115, in _nearest | r_idx, dist = _next_nonoverlapping(df_to_find_nearest_in.End, | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 62, in _next_nonoverlapping | r_idx, dist = nearest_next_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 34, in sorted_nearest.src.sorted_nearest.nearest_next_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_nearest( | nearest_how='downstream', | overlap=True, | strandedness=False, | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:11 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:12 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:101 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 | (and 64 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2TABIxIFJQNAAB0AAU=') as a decorator on your test case +---------------- 3 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 359, in test_nearest | compare_results_nearest(bedtools_df, result) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 107, in compare_results_nearest | assert_df_equal(result_df, bedtools_df) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/helpers.py", line 60, in assert_df_equal | pd.testing.assert_frame_equal(df1, df2) | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 1279, in assert_frame_equal | assert_series_equal( | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 975, in assert_series_equal | assert_attr_equal("dtype", left, right, obj=f"Attributes of {obj}") | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 421, in assert_attr_equal | raise_assert_detail(obj, msg, left_attr, right_attr) | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 614, in raise_assert_detail | raise AssertionError(msg) | AssertionError: Attributes of DataFrame.iloc[:, 4] (column name="Distance") are different | | Attribute "dtype" are different | [left]: int32 | [right]: int64 | Falsifying example: test_nearest( | nearest_how='downstream', | overlap=True, | strandedness=False, | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/init.py:174 | (and 453 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2TABIwoFBgAAABtAAQ=') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptv81q8cs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptv81q8cs/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7qgsgdt_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7qgsgdt_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqoem44ct/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqoem44ct/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplhxf8v7o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplhxf8v7o/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 292 + 0 1 chr1 9634076 9637165 - 0 2 chr5 9634076 9636630 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 292 | a | 0 | ... | | chr1 | 9634076 | 9637165 | a | 0 | ... | | chr5 | 9634076 | 9636630 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 292 + 0 2 chr5 9634076 9636630 - 0 1 chr1 9634076 9637165 - 0 df2 Chromosome Start End Strand Distance 0 chr1 2 292 + 0 2 chr5 9634076 9636630 - 0 1 chr1 9634076 9637165 - 0 Actual Chromosome Start End Strand Distance 0 chr1 2 292 + 0 1 chr1 9634076 9637165 - 0 2 chr5 9634076 9636630 - 0 Expected Chromosome Start End Strand Distance 0 chr1 2 292 + 0 1 chr1 9634076 9637165 - 0 2 chr5 9634076 9636630 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfoximi8v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfoximi8v/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpr2zs6po5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr2zs6po5/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4 5 + 0 1 chr1 4 5 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4 | 5 | a | 0 | ... | | chr1 | 4 | 5 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 4 5 + 0 1 chr1 4 5 - 0 df2 Chromosome Start End Strand Distance 0 chr1 4 5 + 0 1 chr1 4 5 - 0 Actual Chromosome Start End Strand Distance 0 chr1 4 5 + 0 1 chr1 4 5 - 0 Expected Chromosome Start End Strand Distance 0 chr1 4 5 + 0 1 chr1 4 5 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp62n9_eiu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp62n9_eiu/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4 5 + 0 1 chr1 4 5 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4 | 5 | a | 0 | ... | | chr1 | 4 | 5 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 4 5 + 0 1 chr1 4 5 + 0 df2 Chromosome Start End Strand Distance 0 chr1 4 5 + 0 1 chr1 4 5 + 0 Actual Chromosome Start End Strand Distance 0 chr1 4 5 + 0 1 chr1 4 5 + 0 Expected Chromosome Start End Strand Distance 0 chr1 4 5 + 0 1 chr1 4 5 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpj_51yvwn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj_51yvwn/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe01jy3qg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe01jy3qg/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 523224 526184 - 0 1 chr1 3238862 3240565 + 0 2 chr1 3238862 3241822 + 0 3 chr1 4684104 4687064 + 0 4 chr1 7011480 7014440 - 0 5 chr13 3238862 3241822 - 0 6 chr7 3238862 3241822 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3238862 | 3241822 | a | 0 | ... | | chr1 | 4684104 | 4687064 | a | 0 | ... | | chr1 | 3238862 | 3240565 | a | 0 | ... | | chr1 | 7011480 | 7014440 | a | 0 | ... | | chr1 | 523224 | 526184 | a | 0 | ... | | chr7 | 3238862 | 3241822 | a | 0 | ... | | chr13 | 3238862 | 3241822 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 7 rows and 12 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 4 chr1 523224 526184 - 0 2 chr1 3238862 3240565 + 0 0 chr1 3238862 3241822 + 0 5 chr7 3238862 3241822 + 0 6 chr13 3238862 3241822 - 0 1 chr1 4684104 4687064 + 0 3 chr1 7011480 7014440 - 0 df2 Chromosome Start End Strand Distance 0 chr1 523224 526184 - 0 1 chr1 3238862 3240565 + 0 2 chr1 3238862 3241822 + 0 5 chr13 3238862 3241822 - 0 6 chr7 3238862 3241822 + 0 3 chr1 4684104 4687064 + 0 4 chr1 7011480 7014440 - 0 Actual Chromosome Start End Strand Distance 0 chr1 523224 526184 - 0 1 chr1 3238862 3240565 + 0 2 chr1 3238862 3241822 + 0 3 chr1 4684104 4687064 + 0 4 chr1 7011480 7014440 - 0 5 chr13 3238862 3241822 - 0 6 chr7 3238862 3241822 + 0 Expected Chromosome Start End Strand Distance 0 chr1 523224 526184 - 0 1 chr1 3238862 3240565 + 0 2 chr1 3238862 3241822 + 0 3 chr1 4684104 4687064 + 0 4 chr1 7011480 7014440 - 0 5 chr13 3238862 3241822 - 0 6 chr7 3238862 3241822 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=7, step=1) Expected index RangeIndex(start=0, stop=7, step=1) index equal [ True True True True True True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppwdjehiv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppwdjehiv/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 523224 526184 - 0 1 chr1 3238862 3241822 + 0 2 chr1 3238862 3241822 + 0 3 chr1 4684104 4686018 + 0 4 chr1 7011480 7014440 - 0 5 chr13 3238862 3241822 - 0 6 chr7 3238862 3241822 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3238862 | 3241822 | a | 0 | ... | | chr1 | 4684104 | 4686018 | a | 0 | ... | | chr1 | 3238862 | 3241822 | a | 0 | ... | | chr1 | 7011480 | 7014440 | a | 0 | ... | | chr1 | 523224 | 526184 | a | 0 | ... | | chr7 | 3238862 | 3241822 | a | 0 | ... | | chr13 | 3238862 | 3241822 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 7 rows and 12 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 4 chr1 523224 526184 - 0 0 chr1 3238862 3241822 + 0 2 chr1 3238862 3241822 + 0 5 chr7 3238862 3241822 + 0 6 chr13 3238862 3241822 - 0 1 chr1 4684104 4686018 + 0 3 chr1 7011480 7014440 - 0 df2 Chromosome Start End Strand Distance 0 chr1 523224 526184 - 0 1 chr1 3238862 3241822 + 0 2 chr1 3238862 3241822 + 0 5 chr13 3238862 3241822 - 0 6 chr7 3238862 3241822 + 0 3 chr1 4684104 4686018 + 0 4 chr1 7011480 7014440 - 0 Actual Chromosome Start End Strand Distance 0 chr1 523224 526184 - 0 1 chr1 3238862 3241822 + 0 2 chr1 3238862 3241822 + 0 3 chr1 4684104 4686018 + 0 4 chr1 7011480 7014440 - 0 5 chr13 3238862 3241822 - 0 6 chr7 3238862 3241822 + 0 Expected Chromosome Start End Strand Distance 0 chr1 523224 526184 - 0 1 chr1 3238862 3241822 + 0 2 chr1 3238862 3241822 + 0 3 chr1 4684104 4686018 + 0 4 chr1 7011480 7014440 - 0 5 chr13 3238862 3241822 - 0 6 chr7 3238862 3241822 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=7, step=1) Expected index RangeIndex(start=0, stop=7, step=1) index equal [ True True True True True True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp11d8bk9c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp11d8bk9c/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 523224 526184 - 0 1 chr1 3238862 3241822 + 0 2 chr1 3238862 3241822 + 0 3 chr1 4684104 4686018 + 0 4 chr1 7011480 7014440 - 0 5 chr13 3238862 3241822 - 0 6 chr7 3238862 3241822 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3238862 | 3241822 | a | 0 | ... | | chr1 | 4684104 | 4686018 | a | 0 | ... | | chr1 | 3238862 | 3241822 | a | 0 | ... | | chr1 | 7011480 | 7014440 | a | 0 | ... | | chr1 | 523224 | 526184 | a | 0 | ... | | chr7 | 3238862 | 3241822 | a | 0 | ... | | chr13 | 3238862 | 3241822 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 7 rows and 12 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 4 chr1 523224 526184 - 0 0 chr1 3238862 3241822 + 0 2 chr1 3238862 3241822 + 0 5 chr7 3238862 3241822 + 0 6 chr13 3238862 3241822 - 0 1 chr1 4684104 4686018 + 0 3 chr1 7011480 7014440 - 0 df2 Chromosome Start End Strand Distance 0 chr1 523224 526184 - 0 1 chr1 3238862 3241822 + 0 2 chr1 3238862 3241822 + 0 5 chr13 3238862 3241822 - 0 6 chr7 3238862 3241822 + 0 3 chr1 4684104 4686018 + 0 4 chr1 7011480 7014440 - 0 Actual Chromosome Start End Strand Distance 0 chr1 523224 526184 - 0 1 chr1 3238862 3241822 + 0 2 chr1 3238862 3241822 + 0 3 chr1 4684104 4686018 + 0 4 chr1 7011480 7014440 - 0 5 chr13 3238862 3241822 - 0 6 chr7 3238862 3241822 + 0 Expected Chromosome Start End Strand Distance 0 chr1 523224 526184 - 0 1 chr1 3238862 3241822 + 0 2 chr1 3238862 3241822 + 0 3 chr1 4684104 4686018 + 0 4 chr1 7011480 7014440 - 0 5 chr13 3238862 3241822 - 0 6 chr7 3238862 3241822 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=7, step=1) Expected index RangeIndex(start=0, stop=7, step=1) index equal [ True True True True True True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpk0yu5i3x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk0yu5i3x/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjwyl42_h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjwyl42_h/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpj52ey4un/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj52ey4un/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_tocg4dy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_tocg4dy/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_kwjio5b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_kwjio5b/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_x22pctw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_x22pctw/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpufywxjr4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpufywxjr4/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1_7ctkk_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1_7ctkk_/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp12u9h8ox/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp12u9h8ox/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8gt02b0f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8gt02b0f/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwn6i575k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwn6i575k/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbr67wa7l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbr67wa7l/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp47g9xnww/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp47g9xnww/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp90_yzx73/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp90_yzx73/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpn6p2rpe9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn6p2rpe9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpaf8v7ldq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaf8v7ldq/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphn8h5odw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphn8h5odw/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp22770_ux/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp22770_ux/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3oo_9f_i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3oo_9f_i/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpf6zucnn6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf6zucnn6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyd6c13ch/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyd6c13ch/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8tgka_04/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8tgka_04/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2mnd3ou3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2mnd3ou3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpih0nyi3y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpih0nyi3y/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppgyld7gc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppgyld7gc/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4bv3vmme/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4bv3vmme/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdd797b5w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdd797b5w/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp52t7yfee/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp52t7yfee/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2p6crcpm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2p6crcpm/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpefhrsq55/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpefhrsq55/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuu68gwuw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuu68gwuw/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpm1bfq95e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm1bfq95e/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7u4tlx7y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7u4tlx7y/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6e33oqy4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6e33oqy4/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcs6zn0s3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcs6zn0s3/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptvbrrzg0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptvbrrzg0/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1tq723ww/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1tq723ww/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1xw7edwn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1xw7edwn/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpobvr_4nq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpobvr_4nq/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqw4c5gc5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqw4c5gc5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdhenjveo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdhenjveo/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpeqt8r9t1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpeqt8r9t1/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgz5rlr8n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgz5rlr8n/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 258 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 258 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 258 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 258 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 258 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 258 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpaup87bof/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaup87bof/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpztpoundj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpztpoundj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcxl9vjsx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcxl9vjsx/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5c8y7j4v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5c8y7j4v/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdrgau1jh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdrgau1jh/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8wkf_ld7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8wkf_ld7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsftm7won/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsftm7won/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjppg0m8c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjppg0m8c/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpphkgxxwj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpphkgxxwj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplqkehyt3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplqkehyt3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1tfn2sl1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1tfn2sl1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpowp2mh8v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpowp2mh8v/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxdhk77qs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxdhk77qs/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0j9otw05/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0j9otw05/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe51e5x0m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe51e5x0m/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpk7j3e7c3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk7j3e7c3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8h70qky2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8h70qky2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9epnlexi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9epnlexi/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5fnohfg9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5fnohfg9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpi_zuugh2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi_zuugh2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgjrehnba/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgjrehnba/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplgkli63m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplgkli63m/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpr6yyojyc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr6yyojyc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcdj4ta9a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcdj4ta9a/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpv1ze1432/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv1ze1432/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp41ak3ozn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp41ak3ozn/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpc_bkvmus/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc_bkvmus/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpspl1_7lx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpspl1_7lx/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpq4_9zamb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq4_9zamb/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsq95s2ix/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsq95s2ix/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp24y7v24c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp24y7v24c/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpq_on46h4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq_on46h4/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpj91je329/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj91je329/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgo8nnxel/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgo8nnxel/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0z5fgsft/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0z5fgsft/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmph1u31wjq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph1u31wjq/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7fh8xa6k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7fh8xa6k/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpf8ymvnyd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf8ymvnyd/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpohi8rygk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpohi8rygk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4atd5mhy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4atd5mhy/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwee0deo1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwee0deo1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7ome0ioa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7ome0ioa/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmk2uih9z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmk2uih9z/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsq6faxzu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsq6faxzu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3yp2mnyq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3yp2mnyq/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptbi_j9rx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptbi_j9rx/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ___________ test_three_in_a_row[strandedness_chain23-method_chain23] ___________ [gw6] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', False), method_chain = ('nearest', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('nearest', 'overlap'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:53 E (and 28 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2TAAIyMUBpOAElGWZ13p1wUmBgADe4Cbw==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain61-method_chain61] ___________ [gw9] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', 'same') method_chain = ('set_intersect', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('set_intersect', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E /usr/lib/python3/dist-packages/natsort/utils.py:344 E (and 103 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2CMDjr5SVh0JSMDIwMmAABUdwM9') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') __________________________ test_subtraction[opposite] __________________________ [gw1] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness = 'opposite' @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness", ["same", "opposite", False]) # tests/test_binary.py:286: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:308: in test_subtraction result = gr.subtract(gr2, strandedness=strandedness) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_subtraction( E # The test always failed when commented parts were varied together. E strandedness='opposite', E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., # or any other generated value E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., # or any other generated value E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2TABIxYxAAAZAAD') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp57uil48u/f1.bed -b /tmp/tmp57uil48u/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpnq6qx0dn/f1.bed -b /tmp/tmpnq6qx0dn/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp9dzc3xg8/f1.bed -b /tmp/tmp9dzc3xg8/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpznxm7diu/f1.bed -b /tmp/tmpznxm7diu/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpw5tlxmw5/f1.bed -b /tmp/tmpw5tlxmw5/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp683d3pmo/f1.bed -b /tmp/tmp683d3pmo/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp0rq5kf8t/f1.bed -b /tmp/tmp0rq5kf8t/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp4v965pba/f1.bed -b /tmp/tmp4v965pba/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp_fwyaayr/f1.bed -b /tmp/tmp_fwyaayr/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp9ky3_4b_/f1.bed -b /tmp/tmp9ky3_4b_/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpdsbw121y/f1.bed -b /tmp/tmpdsbw121y/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpp089sgdk/f1.bed -b /tmp/tmpp089sgdk/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp32pazdln/f1.bed -b /tmp/tmp32pazdln/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpze5j9ukn/f1.bed -b /tmp/tmpze5j9ukn/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp5avhsdom/f1.bed -b /tmp/tmp5avhsdom/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpa1_bi5yc/f1.bed -b /tmp/tmpa1_bi5yc/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmptjl5yqlj/f1.bed -b /tmp/tmptjl5yqlj/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpk0vclrye/f1.bed -b /tmp/tmpk0vclrye/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp_k5qyu5b/f1.bed -b /tmp/tmp_k5qyu5b/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpuit_y7fr/f1.bed -b /tmp/tmpuit_y7fr/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpmbwbcx_m/f1.bed -b /tmp/tmpmbwbcx_m/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmprozgyl3r/f1.bed -b /tmp/tmprozgyl3r/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp3njazo7c/f1.bed -b /tmp/tmp3njazo7c/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp08gl1shm/f1.bed -b /tmp/tmp08gl1shm/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp4nh90jhp/f1.bed -b /tmp/tmp4nh90jhp/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp_re3u2o0/f1.bed -b /tmp/tmp_re3u2o0/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpq06vwsk7/f1.bed -b /tmp/tmpq06vwsk7/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp1q1gaoec/f1.bed -b /tmp/tmp1q1gaoec/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpvnay6hpl/f1.bed -b /tmp/tmpvnay6hpl/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpajbjhbzh/f1.bed -b /tmp/tmpajbjhbzh/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmppiawdfml/f1.bed -b /tmp/tmppiawdfml/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpoak_xvud/f1.bed -b /tmp/tmpoak_xvud/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpf0rlu26a/f1.bed -b /tmp/tmpf0rlu26a/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp6odjifzj/f1.bed -b /tmp/tmp6odjifzj/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpnsgzrp3b/f1.bed -b /tmp/tmpnsgzrp3b/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmps8vhxb4y/f1.bed -b /tmp/tmps8vhxb4y/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp4pzqc34a/f1.bed -b /tmp/tmp4pzqc34a/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpdwmzqqxe/f1.bed -b /tmp/tmpdwmzqqxe/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp9vbzxhtt/f1.bed -b /tmp/tmp9vbzxhtt/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpk_3vy_s2/f1.bed -b /tmp/tmpk_3vy_s2/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpyfx8gi4q/f1.bed -b /tmp/tmpyfx8gi4q/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpazkh4mk5/f1.bed -b /tmp/tmpazkh4mk5/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpc7_ocoa0/f1.bed -b /tmp/tmpc7_ocoa0/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpe78wuww2/f1.bed -b /tmp/tmpe78wuww2/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpcey6jpbn/f1.bed -b /tmp/tmpcey6jpbn/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpmj185w1l/f1.bed -b /tmp/tmpmj185w1l/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpey_lh1no/f1.bed -b /tmp/tmpey_lh1no/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpz7lbq910/f1.bed -b /tmp/tmpz7lbq910/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpc7odo8kv/f1.bed -b /tmp/tmpc7odo8kv/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp0xwxdmmc/f1.bed -b /tmp/tmp0xwxdmmc/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmperuwmk36/f1.bed -b /tmp/tmperuwmk36/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpbe1yw4dt/f1.bed -b /tmp/tmpbe1yw4dt/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmph8qdhxc4/f1.bed -b /tmp/tmph8qdhxc4/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpv6908z70/f1.bed -b /tmp/tmpv6908z70/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpueigdiy_/f1.bed -b /tmp/tmpueigdiy_/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpx8sur0e9/f1.bed -b /tmp/tmpx8sur0e9/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpwel00nja/f1.bed -b /tmp/tmpwel00nja/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp4fhob_af/f1.bed -b /tmp/tmp4fhob_af/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmplm_tks7v/f1.bed -b /tmp/tmplm_tks7v/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpw_h5te4l/f1.bed -b /tmp/tmpw_h5te4l/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmppu1u8era/f1.bed -b /tmp/tmppu1u8era/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp6snp93x6/f1.bed -b /tmp/tmp6snp93x6/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp9aisrq4c/f1.bed -b /tmp/tmp9aisrq4c/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp9ddhhrcb/f1.bed -b /tmp/tmp9ddhhrcb/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp1fahtqi6/f1.bed -b /tmp/tmp1fahtqi6/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpgli_jl54/f1.bed -b /tmp/tmpgli_jl54/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp_vgsnst2/f1.bed -b /tmp/tmp_vgsnst2/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp7us7bftc/f1.bed -b /tmp/tmp7us7bftc/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpodn9_afm/f1.bed -b /tmp/tmpodn9_afm/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp51t7jawb/f1.bed -b /tmp/tmp51t7jawb/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpjb7vjvah/f1.bed -b /tmp/tmpjb7vjvah/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpbh30txmu/f1.bed -b /tmp/tmpbh30txmu/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpp0n3ajnp/f1.bed -b /tmp/tmpp0n3ajnp/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpuprj1wzf/f1.bed -b /tmp/tmpuprj1wzf/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp56m4hc47/f1.bed -b /tmp/tmp56m4hc47/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp86xmzl_2/f1.bed -b /tmp/tmp86xmzl_2/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp5zje79q0/f1.bed -b /tmp/tmp5zje79q0/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpgxvmswp9/f1.bed -b /tmp/tmpgxvmswp9/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp26qms6yw/f1.bed -b /tmp/tmp26qms6yw/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp3s90mopp/f1.bed -b /tmp/tmp3s90mopp/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpkm1ms__7/f1.bed -b /tmp/tmpkm1ms__7/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp1pt_9tlm/f1.bed -b /tmp/tmp1pt_9tlm/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmprsm9bq2l/f1.bed -b /tmp/tmprsm9bq2l/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp3trw03x2/f1.bed -b /tmp/tmp3trw03x2/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp3y21obbn/f1.bed -b /tmp/tmp3y21obbn/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp_mg3nzvf/f1.bed -b /tmp/tmp_mg3nzvf/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpu0a3yahz/f1.bed -b /tmp/tmpu0a3yahz/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpinm9cdj4/f1.bed -b /tmp/tmpinm9cdj4/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpfg24jsv4/f1.bed -b /tmp/tmpfg24jsv4/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpv9d7ett6/f1.bed -b /tmp/tmpv9d7ett6/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpjz6t7tkw/f1.bed -b /tmp/tmpjz6t7tkw/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp_8i0ext2/f1.bed -b /tmp/tmp_8i0ext2/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp8arjz7c5/f1.bed -b /tmp/tmp8arjz7c5/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpo_09p4f1/f1.bed -b /tmp/tmpo_09p4f1/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpgl4nagp_/f1.bed -b /tmp/tmpgl4nagp_/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp9p5hm6bn/f1.bed -b /tmp/tmp9p5hm6bn/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpgic3scej/f1.bed -b /tmp/tmpgic3scej/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp3fpxo5qu/f1.bed -b /tmp/tmp3fpxo5qu/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpegowrt_u/f1.bed -b /tmp/tmpegowrt_u/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp85y0j2m2/f1.bed -b /tmp/tmp85y0j2m2/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpqkwz5gt5/f1.bed -b /tmp/tmpqkwz5gt5/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp053sokq5/f1.bed -b /tmp/tmp053sokq5/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp1hgolkst/f1.bed -b /tmp/tmp1hgolkst/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpwszkiilj/f1.bed -b /tmp/tmpwszkiilj/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp6obq3gvj/f1.bed -b /tmp/tmp6obq3gvj/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpozvp9o6x/f1.bed -b /tmp/tmpozvp9o6x/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmppezvcp70/f1.bed -b /tmp/tmppezvcp70/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpdgb6kqiy/f1.bed -b /tmp/tmpdgb6kqiy/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpfwza06f1/f1.bed -b /tmp/tmpfwza06f1/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmppciygt31/f1.bed -b /tmp/tmppciygt31/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpk1qw7xd0/f1.bed -b /tmp/tmpk1qw7xd0/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpak0bh9di/f1.bed -b /tmp/tmpak0bh9di/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmphac_cn4o/f1.bed -b /tmp/tmphac_cn4o/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpvf8d325j/f1.bed -b /tmp/tmpvf8d325j/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp92jbmwhi/f1.bed -b /tmp/tmp92jbmwhi/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpumicw9hr/f1.bed -b /tmp/tmpumicw9hr/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp4pr7trur/f1.bed -b /tmp/tmp4pr7trur/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp1atnv_71/f1.bed -b /tmp/tmp1atnv_71/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpts6nm5an/f1.bed -b /tmp/tmpts6nm5an/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpbpo2c8aq/f1.bed -b /tmp/tmpbpo2c8aq/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp_kl12dmb/f1.bed -b /tmp/tmp_kl12dmb/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpjjkf9r5e/f1.bed -b /tmp/tmpjjkf9r5e/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpm3uxlbma/f1.bed -b /tmp/tmpm3uxlbma/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp59wpww43/f1.bed -b /tmp/tmp59wpww43/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmphze_rzcf/f1.bed -b /tmp/tmphze_rzcf/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmplm3ijuo2/f1.bed -b /tmp/tmplm3ijuo2/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpx8lrxjbh/f1.bed -b /tmp/tmpx8lrxjbh/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp0ubpd1eg/f1.bed -b /tmp/tmp0ubpd1eg/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp8dtejjbk/f1.bed -b /tmp/tmp8dtejjbk/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpnk9goyt_/f1.bed -b /tmp/tmpnk9goyt_/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpeuik0210/f1.bed -b /tmp/tmpeuik0210/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp00mne4y8/f1.bed -b /tmp/tmp00mne4y8/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp_f5o5i4w/f1.bed -b /tmp/tmp_f5o5i4w/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpmwe3uldr/f1.bed -b /tmp/tmpmwe3uldr/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp4ocmuiyz/f1.bed -b /tmp/tmp4ocmuiyz/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpuoz2spnp/f1.bed -b /tmp/tmpuoz2spnp/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp2lx_fq_w/f1.bed -b /tmp/tmp2lx_fq_w/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpt_60oscc/f1.bed -b /tmp/tmpt_60oscc/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpue642r0u/f1.bed -b /tmp/tmpue642r0u/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp2_27ep8a/f1.bed -b /tmp/tmp2_27ep8a/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmps75z_ufd/f1.bed -b /tmp/tmps75z_ufd/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpsg5hxvcg/f1.bed -b /tmp/tmpsg5hxvcg/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpase7b3_7/f1.bed -b /tmp/tmpase7b3_7/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpsx9nur8k/f1.bed -b /tmp/tmpsx9nur8k/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpth7f6klc/f1.bed -b /tmp/tmpth7f6klc/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp7vvscnsy/f1.bed -b /tmp/tmp7vvscnsy/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpbhcxvk82/f1.bed -b /tmp/tmpbhcxvk82/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpx8q4zwpa/f1.bed -b /tmp/tmpx8q4zwpa/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmppsgoxauq/f1.bed -b /tmp/tmppsgoxauq/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpu6m7laly/f1.bed -b /tmp/tmpu6m7laly/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpo5n85abn/f1.bed -b /tmp/tmpo5n85abn/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp0r7avog3/f1.bed -b /tmp/tmp0r7avog3/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpg9m9lkae/f1.bed -b /tmp/tmpg9m9lkae/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpzq6_2l6n/f1.bed -b /tmp/tmpzq6_2l6n/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpfykn3p77/f1.bed -b /tmp/tmpfykn3p77/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpqiwc7eue/f1.bed -b /tmp/tmpqiwc7eue/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp65_bbnrs/f1.bed -b /tmp/tmp65_bbnrs/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpc50p004e/f1.bed -b /tmp/tmpc50p004e/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp2_be__tj/f1.bed -b /tmp/tmp2_be__tj/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp0_l_i3nn/f1.bed -b /tmp/tmp0_l_i3nn/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp8gcg9fvy/f1.bed -b /tmp/tmp8gcg9fvy/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpak4lglot/f1.bed -b /tmp/tmpak4lglot/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpg526dw5j/f1.bed -b /tmp/tmpg526dw5j/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpv08oxuco/f1.bed -b /tmp/tmpv08oxuco/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpz11v3oix/f1.bed -b /tmp/tmpz11v3oix/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp9omz15ow/f1.bed -b /tmp/tmp9omz15ow/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpqbygg39m/f1.bed -b /tmp/tmpqbygg39m/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpdsslm2b1/f1.bed -b /tmp/tmpdsslm2b1/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpx9828slt/f1.bed -b /tmp/tmpx9828slt/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp0mfna_ye/f1.bed -b /tmp/tmp0mfna_ye/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp772qgq5c/f1.bed -b /tmp/tmp772qgq5c/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpbb57k0ts/f1.bed -b /tmp/tmpbb57k0ts/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpkdbah42b/f1.bed -b /tmp/tmpkdbah42b/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpc4jdjhbu/f1.bed -b /tmp/tmpc4jdjhbu/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp5a9ls134/f1.bed -b /tmp/tmp5a9ls134/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpndlhssas/f1.bed -b /tmp/tmpndlhssas/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpc3mq302f/f1.bed -b /tmp/tmpc3mq302f/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmps73xfj42/f1.bed -b /tmp/tmps73xfj42/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpvy8f0jkb/f1.bed -b /tmp/tmpvy8f0jkb/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpgcmyp13i/f1.bed -b /tmp/tmpgcmyp13i/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpecy_7eg6/f1.bed -b /tmp/tmpecy_7eg6/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpe1xkwcz4/f1.bed -b /tmp/tmpe1xkwcz4/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpiyexz513/f1.bed -b /tmp/tmpiyexz513/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmplue5ncth/f1.bed -b /tmp/tmplue5ncth/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpma65svr7/f1.bed -b /tmp/tmpma65svr7/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpzhtwma_c/f1.bed -b /tmp/tmpzhtwma_c/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmphnwo59o0/f1.bed -b /tmp/tmphnwo59o0/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp8n3ieetz/f1.bed -b /tmp/tmp8n3ieetz/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp7hgods_y/f1.bed -b /tmp/tmp7hgods_y/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp6npl1p8e/f1.bed -b /tmp/tmp6npl1p8e/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpqe9uokrw/f1.bed -b /tmp/tmpqe9uokrw/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpaynygswe/f1.bed -b /tmp/tmpaynygswe/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp27agl_yu/f1.bed -b /tmp/tmp27agl_yu/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp4zhwridf/f1.bed -b /tmp/tmp4zhwridf/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp17hix0g8/f1.bed -b /tmp/tmp17hix0g8/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmputy636dx/f1.bed -b /tmp/tmputy636dx/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp6xzrkd1v/f1.bed -b /tmp/tmp6xzrkd1v/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpnm_9354f/f1.bed -b /tmp/tmpnm_9354f/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp1u0kcqko/f1.bed -b /tmp/tmp1u0kcqko/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp6jz7z3p2/f1.bed -b /tmp/tmp6jz7z3p2/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpv9y_pyo3/f1.bed -b /tmp/tmpv9y_pyo3/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp8g6n6ur_/f1.bed -b /tmp/tmp8g6n6ur_/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpxf3swhe5/f1.bed -b /tmp/tmpxf3swhe5/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp73hr7ozx/f1.bed -b /tmp/tmp73hr7ozx/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpq3oiljvf/f1.bed -b /tmp/tmpq3oiljvf/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp1acvzriy/f1.bed -b /tmp/tmp1acvzriy/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpjir6_gh3/f1.bed -b /tmp/tmpjir6_gh3/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpn6wp_fi0/f1.bed -b /tmp/tmpn6wp_fi0/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp8xlliknb/f1.bed -b /tmp/tmp8xlliknb/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpihozupsb/f1.bed -b /tmp/tmpihozupsb/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpgzinmcof/f1.bed -b /tmp/tmpgzinmcof/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpcgjjnloj/f1.bed -b /tmp/tmpcgjjnloj/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpjpd8avrb/f1.bed -b /tmp/tmpjpd8avrb/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpsvdc2pr_/f1.bed -b /tmp/tmpsvdc2pr_/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpyisdrh8e/f1.bed -b /tmp/tmpyisdrh8e/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmptpj5h6m3/f1.bed -b /tmp/tmptpj5h6m3/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp5d1i869t/f1.bed -b /tmp/tmp5d1i869t/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp98ehnnu1/f1.bed -b /tmp/tmp98ehnnu1/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp2vn2jzc0/f1.bed -b /tmp/tmp2vn2jzc0/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpjn0yu0c5/f1.bed -b /tmp/tmpjn0yu0c5/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmprsmf1j3t/f1.bed -b /tmp/tmprsmf1j3t/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpbgtz7d7n/f1.bed -b /tmp/tmpbgtz7d7n/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmptgp44cbu/f1.bed -b /tmp/tmptgp44cbu/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpo9_6__p6/f1.bed -b /tmp/tmpo9_6__p6/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpn9krrp9v/f1.bed -b /tmp/tmpn9krrp9v/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpwkf2pxe9/f1.bed -b /tmp/tmpwkf2pxe9/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpccf4n51d/f1.bed -b /tmp/tmpccf4n51d/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp4rdvmhvi/f1.bed -b /tmp/tmp4rdvmhvi/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpo2njbucg/f1.bed -b /tmp/tmpo2njbucg/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpf2z1ryq1/f1.bed -b /tmp/tmpf2z1ryq1/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpf3r4uue8/f1.bed -b /tmp/tmpf3r4uue8/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpcdvu2ydp/f1.bed -b /tmp/tmpcdvu2ydp/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp613hoiab/f1.bed -b /tmp/tmp613hoiab/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpmhrd8uwv/f1.bed -b /tmp/tmpmhrd8uwv/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpgi0hdvyu/f1.bed -b /tmp/tmpgi0hdvyu/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpay48k9vv/f1.bed -b /tmp/tmpay48k9vv/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp58l7doib/f1.bed -b /tmp/tmp58l7doib/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpe39lvcdp/f1.bed -b /tmp/tmpe39lvcdp/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp4zk5hqn8/f1.bed -b /tmp/tmp4zk5hqn8/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpd1cv8uv6/f1.bed -b /tmp/tmpd1cv8uv6/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp7cbk2fou/f1.bed -b /tmp/tmp7cbk2fou/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmplhd5eo9t/f1.bed -b /tmp/tmplhd5eo9t/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpmuntmjby/f1.bed -b /tmp/tmpmuntmjby/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpb2hrtinh/f1.bed -b /tmp/tmpb2hrtinh/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp7tg19w0b/f1.bed -b /tmp/tmp7tg19w0b/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpruhn2_dm/f1.bed -b /tmp/tmpruhn2_dm/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpx6tt4xge/f1.bed -b /tmp/tmpx6tt4xge/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmphmxfm4hi/f1.bed -b /tmp/tmphmxfm4hi/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpubyr49ee/f1.bed -b /tmp/tmpubyr49ee/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpbaciawz3/f1.bed -b /tmp/tmpbaciawz3/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp9cim79fz/f1.bed -b /tmp/tmp9cim79fz/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpj279vgou/f1.bed -b /tmp/tmpj279vgou/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp9tx23f3p/f1.bed -b /tmp/tmp9tx23f3p/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpjwpo897e/f1.bed -b /tmp/tmpjwpo897e/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpcvrswzk5/f1.bed -b /tmp/tmpcvrswzk5/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp6qw49j0v/f1.bed -b /tmp/tmp6qw49j0v/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpyt49mibi/f1.bed -b /tmp/tmpyt49mibi/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpof26zmeu/f1.bed -b /tmp/tmpof26zmeu/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp9r5rvurv/f1.bed -b /tmp/tmp9r5rvurv/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp67_xfz5q/f1.bed -b /tmp/tmp67_xfz5q/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpfjzmw4gx/f1.bed -b /tmp/tmpfjzmw4gx/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmptwyxlij8/f1.bed -b /tmp/tmptwyxlij8/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpo62b8nuc/f1.bed -b /tmp/tmpo62b8nuc/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpnnz0deu7/f1.bed -b /tmp/tmpnnz0deu7/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpgpbhyd58/f1.bed -b /tmp/tmpgpbhyd58/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpczsq0sv0/f1.bed -b /tmp/tmpczsq0sv0/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpkhlrod3x/f1.bed -b /tmp/tmpkhlrod3x/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp1s5r65ky/f1.bed -b /tmp/tmp1s5r65ky/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpm26afe6_/f1.bed -b /tmp/tmpm26afe6_/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp6nk41e2n/f1.bed -b /tmp/tmp6nk41e2n/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpizaj66jb/f1.bed -b /tmp/tmpizaj66jb/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpmy8mqf1_/f1.bed -b /tmp/tmpmy8mqf1_/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpqdifwukm/f1.bed -b /tmp/tmpqdifwukm/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpjqf2_bup/f1.bed -b /tmp/tmpjqf2_bup/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpoj7ld8ur/f1.bed -b /tmp/tmpoj7ld8ur/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpp0wgx9bw/f1.bed -b /tmp/tmpp0wgx9bw/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpzo0uz87n/f1.bed -b /tmp/tmpzo0uz87n/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpdnjpkegg/f1.bed -b /tmp/tmpdnjpkegg/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmphjb6j4jl/f1.bed -b /tmp/tmphjb6j4jl/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp7b6951un/f1.bed -b /tmp/tmp7b6951un/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpmnqy72lc/f1.bed -b /tmp/tmpmnqy72lc/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp7eqjdsno/f1.bed -b /tmp/tmp7eqjdsno/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpf4yqfr0n/f1.bed -b /tmp/tmpf4yqfr0n/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpg58gkgnm/f1.bed -b /tmp/tmpg58gkgnm/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpdrpv_csy/f1.bed -b /tmp/tmpdrpv_csy/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmph3y4n8vs/f1.bed -b /tmp/tmph3y4n8vs/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpktstc5pq/f1.bed -b /tmp/tmpktstc5pq/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpkbh46k4f/f1.bed -b /tmp/tmpkbh46k4f/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpzsklwkpy/f1.bed -b /tmp/tmpzsklwkpy/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmphtj7upah/f1.bed -b /tmp/tmphtj7upah/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp1ghf5ubd/f1.bed -b /tmp/tmp1ghf5ubd/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpflhqxtc6/f1.bed -b /tmp/tmpflhqxtc6/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpp6z14y9t/f1.bed -b /tmp/tmpp6z14y9t/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpznwpvgu4/f1.bed -b /tmp/tmpznwpvgu4/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpstxgp44s/f1.bed -b /tmp/tmpstxgp44s/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpds8gp76f/f1.bed -b /tmp/tmpds8gp76f/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpiuionlyv/f1.bed -b /tmp/tmpiuionlyv/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp3uscxme3/f1.bed -b /tmp/tmp3uscxme3/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpd4egd6pt/f1.bed -b /tmp/tmpd4egd6pt/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpjjdggfeb/f1.bed -b /tmp/tmpjjdggfeb/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp91kdpi8y/f1.bed -b /tmp/tmp91kdpi8y/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpybb353hx/f1.bed -b /tmp/tmpybb353hx/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmps6wu0x01/f1.bed -b /tmp/tmps6wu0x01/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpq26rk5wv/f1.bed -b /tmp/tmpq26rk5wv/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp1a87ai0z/f1.bed -b /tmp/tmp1a87ai0z/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpeetoqpo7/f1.bed -b /tmp/tmpeetoqpo7/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpfcyp7n7w/f1.bed -b /tmp/tmpfcyp7n7w/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpyn3pkkc5/f1.bed -b /tmp/tmpyn3pkkc5/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmplx0dz446/f1.bed -b /tmp/tmplx0dz446/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp0erhjjxb/f1.bed -b /tmp/tmp0erhjjxb/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp6jtjdzpo/f1.bed -b /tmp/tmp6jtjdzpo/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpujo3jaxz/f1.bed -b /tmp/tmpujo3jaxz/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp_u23p5mt/f1.bed -b /tmp/tmp_u23p5mt/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpduorcr0p/f1.bed -b /tmp/tmpduorcr0p/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpudjr208s/f1.bed -b /tmp/tmpudjr208s/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmprywors4b/f1.bed -b /tmp/tmprywors4b/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpsnb_h7_u/f1.bed -b /tmp/tmpsnb_h7_u/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpvgcdrje1/f1.bed -b /tmp/tmpvgcdrje1/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp7khjitg2/f1.bed -b /tmp/tmp7khjitg2/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpd_rbmv26/f1.bed -b /tmp/tmpd_rbmv26/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp_ok6stks/f1.bed -b /tmp/tmp_ok6stks/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp2tcg1psc/f1.bed -b /tmp/tmp2tcg1psc/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpnwhql816/f1.bed -b /tmp/tmpnwhql816/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp8igqv0_t/f1.bed -b /tmp/tmp8igqv0_t/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp1lclbku4/f1.bed -b /tmp/tmp1lclbku4/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp7i8_467b/f1.bed -b /tmp/tmp7i8_467b/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpxkux134z/f1.bed -b /tmp/tmpxkux134z/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmptpxweu_r/f1.bed -b /tmp/tmptpxweu_r/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpxvux8xnl/f1.bed -b /tmp/tmpxvux8xnl/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpno2o9_nb/f1.bed -b /tmp/tmpno2o9_nb/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp7fil39u3/f1.bed -b /tmp/tmp7fil39u3/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpl1i8453f/f1.bed -b /tmp/tmpl1i8453f/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpfkfvhapi/f1.bed -b /tmp/tmpfkfvhapi/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpzo32iqtp/f1.bed -b /tmp/tmpzo32iqtp/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpnf_1475x/f1.bed -b /tmp/tmpnf_1475x/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpeafv19du/f1.bed -b /tmp/tmpeafv19du/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpk1wt3bsb/f1.bed -b /tmp/tmpk1wt3bsb/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpxsgolifa/f1.bed -b /tmp/tmpxsgolifa/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp_peuusc_/f1.bed -b /tmp/tmp_peuusc_/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpmxzchgui/f1.bed -b /tmp/tmpmxzchgui/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpc7wrzimv/f1.bed -b /tmp/tmpc7wrzimv/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp6thsajan/f1.bed -b /tmp/tmp6thsajan/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpvp2akm3f/f1.bed -b /tmp/tmpvp2akm3f/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpxm419e_o/f1.bed -b /tmp/tmpxm419e_o/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpemystrex/f1.bed -b /tmp/tmpemystrex/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpe_6cshaj/f1.bed -b /tmp/tmpe_6cshaj/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpx9lq5cc_/f1.bed -b /tmp/tmpx9lq5cc_/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpkad6jor6/f1.bed -b /tmp/tmpkad6jor6/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpr6fkd0bn/f1.bed -b /tmp/tmpr6fkd0bn/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp8v4ojaqw/f1.bed -b /tmp/tmp8v4ojaqw/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpnbdye00y/f1.bed -b /tmp/tmpnbdye00y/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpedp_exah/f1.bed -b /tmp/tmpedp_exah/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpaba8sztv/f1.bed -b /tmp/tmpaba8sztv/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpx8yshb1d/f1.bed -b /tmp/tmpx8yshb1d/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpw1dyr07f/f1.bed -b /tmp/tmpw1dyr07f/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpvlzbl2e8/f1.bed -b /tmp/tmpvlzbl2e8/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp0svk_ibf/f1.bed -b /tmp/tmp0svk_ibf/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpccip6qky/f1.bed -b /tmp/tmpccip6qky/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpw55188fe/f1.bed -b /tmp/tmpw55188fe/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpniwtp5zv/f1.bed -b /tmp/tmpniwtp5zv/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpavvuj32r/f1.bed -b /tmp/tmpavvuj32r/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp6e9en2ur/f1.bed -b /tmp/tmp6e9en2ur/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmplrpdv1n9/f1.bed -b /tmp/tmplrpdv1n9/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp4mwfeg4h/f1.bed -b /tmp/tmp4mwfeg4h/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpcj2eocal/f1.bed -b /tmp/tmpcj2eocal/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpzhjfkaz4/f1.bed -b /tmp/tmpzhjfkaz4/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpz3i4pqdn/f1.bed -b /tmp/tmpz3i4pqdn/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpil7h3__2/f1.bed -b /tmp/tmpil7h3__2/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp981y4g22/f1.bed -b /tmp/tmp981y4g22/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpjgjdnfqb/f1.bed -b /tmp/tmpjgjdnfqb/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp6bp9ficw/f1.bed -b /tmp/tmp6bp9ficw/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp7jwhk9zx/f1.bed -b /tmp/tmp7jwhk9zx/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpvln97gy9/f1.bed -b /tmp/tmpvln97gy9/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpiecz_c_u/f1.bed -b /tmp/tmpiecz_c_u/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpc5dlnaom/f1.bed -b /tmp/tmpc5dlnaom/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpbf51xj6x/f1.bed -b /tmp/tmpbf51xj6x/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpgl85474w/f1.bed -b /tmp/tmpgl85474w/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpfx4amqsm/f1.bed -b /tmp/tmpfx4amqsm/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpun77srbt/f1.bed -b /tmp/tmpun77srbt/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpe9igz6ok/f1.bed -b /tmp/tmpe9igz6ok/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp0b0tbakq/f1.bed -b /tmp/tmp0b0tbakq/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpu115xh3n/f1.bed -b /tmp/tmpu115xh3n/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpnshd932o/f1.bed -b /tmp/tmpnshd932o/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpc9dpddsh/f1.bed -b /tmp/tmpc9dpddsh/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpe34s9rwz/f1.bed -b /tmp/tmpe34s9rwz/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpiudkn4sf/f1.bed -b /tmp/tmpiudkn4sf/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp90bgu2tp/f1.bed -b /tmp/tmp90bgu2tp/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp1h1rtqf7/f1.bed -b /tmp/tmp1h1rtqf7/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpf2qu3ug5/f1.bed -b /tmp/tmpf2qu3ug5/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpi75b7s0y/f1.bed -b /tmp/tmpi75b7s0y/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp1lfezsa4/f1.bed -b /tmp/tmp1lfezsa4/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpn9bl0xap/f1.bed -b /tmp/tmpn9bl0xap/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpqjftepyl/f1.bed -b /tmp/tmpqjftepyl/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpsspre_hh/f1.bed -b /tmp/tmpsspre_hh/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpi3vx37_g/f1.bed -b /tmp/tmpi3vx37_g/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp0el83arm/f1.bed -b /tmp/tmp0el83arm/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmphladrwrj/f1.bed -b /tmp/tmphladrwrj/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp4pqm368c/f1.bed -b /tmp/tmp4pqm368c/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp6dbi0lnn/f1.bed -b /tmp/tmp6dbi0lnn/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpncunsbt6/f1.bed -b /tmp/tmpncunsbt6/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpg2qm3ctv/f1.bed -b /tmp/tmpg2qm3ctv/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpy_2bkqqc/f1.bed -b /tmp/tmpy_2bkqqc/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpfv5o8tr5/f1.bed -b /tmp/tmpfv5o8tr5/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpkj7a6egw/f1.bed -b /tmp/tmpkj7a6egw/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpdo0atb8u/f1.bed -b /tmp/tmpdo0atb8u/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpt7pvf6l0/f1.bed -b /tmp/tmpt7pvf6l0/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpv87de05n/f1.bed -b /tmp/tmpv87de05n/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpvz2ecxse/f1.bed -b /tmp/tmpvz2ecxse/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpm7r_wxz_/f1.bed -b /tmp/tmpm7r_wxz_/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpxrg0mfqn/f1.bed -b /tmp/tmpxrg0mfqn/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpavw6g_1g/f1.bed -b /tmp/tmpavw6g_1g/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpa_ckss2h/f1.bed -b /tmp/tmpa_ckss2h/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpe92q0cak/f1.bed -b /tmp/tmpe92q0cak/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpmsj6j0wc/f1.bed -b /tmp/tmpmsj6j0wc/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp3jl3prcq/f1.bed -b /tmp/tmp3jl3prcq/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp3hm0p3_b/f1.bed -b /tmp/tmp3hm0p3_b/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmppl39z7w7/f1.bed -b /tmp/tmppl39z7w7/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpx6hqk22y/f1.bed -b /tmp/tmpx6hqk22y/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting _____________________________ test_set_union[same] _____________________________ [gw0] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness = 'same' @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness", no_opposite) tests/test_binary.py:134: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:149: in test_set_union result = gr.set_union(gr2, strandedness=strandedness) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_set_union( E # The test always failed when commented parts were varied together. E strandedness='same', E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., # or any other generated value E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., # or any other generated value E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2TABIxYxAAAZAAD') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd cat /tmp/tmpwdzje9bl/f1.bed /tmp/tmpwdzje9bl/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpoxxcillf/f1.bed /tmp/tmpoxxcillf/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmptqbo1f1q/f1.bed /tmp/tmptqbo1f1q/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpc_wjm4jb/f1.bed /tmp/tmpc_wjm4jb/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpdam4_gw_/f1.bed /tmp/tmpdam4_gw_/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmph9ax_htt/f1.bed /tmp/tmph9ax_htt/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmptqkbiao6/f1.bed /tmp/tmptqkbiao6/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpakidrqm1/f1.bed /tmp/tmpakidrqm1/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmps3gji1xc/f1.bed /tmp/tmps3gji1xc/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpatzhbu51/f1.bed /tmp/tmpatzhbu51/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpuc3smmel/f1.bed /tmp/tmpuc3smmel/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp9ketbruw/f1.bed /tmp/tmp9ketbruw/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpproyhanx/f1.bed /tmp/tmpproyhanx/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp4lip1m4m/f1.bed /tmp/tmp4lip1m4m/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp144l5vo1/f1.bed /tmp/tmp144l5vo1/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpfgd44fe4/f1.bed /tmp/tmpfgd44fe4/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpe7e12lf3/f1.bed /tmp/tmpe7e12lf3/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp57172qlx/f1.bed /tmp/tmp57172qlx/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpvbijh9jb/f1.bed /tmp/tmpvbijh9jb/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpgnz6ri4j/f1.bed /tmp/tmpgnz6ri4j/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpbz7dn9v7/f1.bed /tmp/tmpbz7dn9v7/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpizab0efo/f1.bed /tmp/tmpizab0efo/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpl8zvxo1n/f1.bed /tmp/tmpl8zvxo1n/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpp5qyxdls/f1.bed /tmp/tmpp5qyxdls/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpnbdxqu4f/f1.bed /tmp/tmpnbdxqu4f/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpjg9du8rx/f1.bed /tmp/tmpjg9du8rx/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpje1h1hfx/f1.bed /tmp/tmpje1h1hfx/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpbre5y0um/f1.bed /tmp/tmpbre5y0um/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpz584ins5/f1.bed /tmp/tmpz584ins5/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpsltxvj3o/f1.bed /tmp/tmpsltxvj3o/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp4yfw25sd/f1.bed /tmp/tmp4yfw25sd/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpckajn823/f1.bed /tmp/tmpckajn823/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp8d8qbwm8/f1.bed /tmp/tmp8d8qbwm8/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpbu2s0ype/f1.bed /tmp/tmpbu2s0ype/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmporyhf_6h/f1.bed /tmp/tmporyhf_6h/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpt0hfrs2h/f1.bed /tmp/tmpt0hfrs2h/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpzle3zo36/f1.bed /tmp/tmpzle3zo36/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpkkktdsfn/f1.bed /tmp/tmpkkktdsfn/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpi5m_cezz/f1.bed /tmp/tmpi5m_cezz/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpyw3g5gwy/f1.bed /tmp/tmpyw3g5gwy/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp92pyoqgi/f1.bed /tmp/tmp92pyoqgi/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp5icdb1h4/f1.bed /tmp/tmp5icdb1h4/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpvb_q2dpy/f1.bed /tmp/tmpvb_q2dpy/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpazqxtqo9/f1.bed /tmp/tmpazqxtqo9/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpwwxifnmi/f1.bed /tmp/tmpwwxifnmi/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpufnw5ba2/f1.bed /tmp/tmpufnw5ba2/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpq76xx460/f1.bed /tmp/tmpq76xx460/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmph4chhvgv/f1.bed /tmp/tmph4chhvgv/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpa3f8ssef/f1.bed /tmp/tmpa3f8ssef/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp47rzcvqo/f1.bed /tmp/tmp47rzcvqo/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmparw1f_k9/f1.bed /tmp/tmparw1f_k9/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmphwic41ks/f1.bed /tmp/tmphwic41ks/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpknvv70q3/f1.bed /tmp/tmpknvv70q3/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp8qhir3ta/f1.bed /tmp/tmp8qhir3ta/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpvm12dr9y/f1.bed /tmp/tmpvm12dr9y/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpplqaf228/f1.bed /tmp/tmpplqaf228/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp75nbk7ab/f1.bed /tmp/tmp75nbk7ab/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp5oqbbdrs/f1.bed /tmp/tmp5oqbbdrs/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpr98bfyio/f1.bed /tmp/tmpr98bfyio/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmps7p_tdi6/f1.bed /tmp/tmps7p_tdi6/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpemx6vu4q/f1.bed /tmp/tmpemx6vu4q/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpnyjh4yjz/f1.bed /tmp/tmpnyjh4yjz/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmptjuu6ls4/f1.bed /tmp/tmptjuu6ls4/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp90jbwoaj/f1.bed /tmp/tmp90jbwoaj/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmproq8nnoo/f1.bed /tmp/tmproq8nnoo/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp9hbuyfmx/f1.bed /tmp/tmp9hbuyfmx/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp23uupta7/f1.bed /tmp/tmp23uupta7/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp8yu4g8st/f1.bed /tmp/tmp8yu4g8st/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmprf_p1t0p/f1.bed /tmp/tmprf_p1t0p/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpqbg0c1nx/f1.bed /tmp/tmpqbg0c1nx/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp30o_ziq3/f1.bed /tmp/tmp30o_ziq3/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpz6ndtdvx/f1.bed /tmp/tmpz6ndtdvx/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp0dgxm49g/f1.bed /tmp/tmp0dgxm49g/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpf5eunjwa/f1.bed /tmp/tmpf5eunjwa/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpmglpspmz/f1.bed /tmp/tmpmglpspmz/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp2fff011_/f1.bed /tmp/tmp2fff011_/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp4dd8j5tm/f1.bed /tmp/tmp4dd8j5tm/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpsf12u9r7/f1.bed /tmp/tmpsf12u9r7/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpl0pnt1zz/f1.bed /tmp/tmpl0pnt1zz/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpy0kl_n70/f1.bed /tmp/tmpy0kl_n70/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp3_v19q3s/f1.bed /tmp/tmp3_v19q3s/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpdl78ldas/f1.bed /tmp/tmpdl78ldas/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmphth3glkm/f1.bed /tmp/tmphth3glkm/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp38fksl7b/f1.bed /tmp/tmp38fksl7b/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp5aln4dwp/f1.bed /tmp/tmp5aln4dwp/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpz6v478mi/f1.bed /tmp/tmpz6v478mi/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpxwthfbrh/f1.bed /tmp/tmpxwthfbrh/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpep_o8tv0/f1.bed /tmp/tmpep_o8tv0/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmplq935jic/f1.bed /tmp/tmplq935jic/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpjoc2xwd5/f1.bed /tmp/tmpjoc2xwd5/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpm5zu3oki/f1.bed /tmp/tmpm5zu3oki/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpemf545ci/f1.bed /tmp/tmpemf545ci/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp6pz8mkcy/f1.bed /tmp/tmp6pz8mkcy/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmprcgdedf2/f1.bed /tmp/tmprcgdedf2/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpi9o4xv40/f1.bed /tmp/tmpi9o4xv40/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmph551oow1/f1.bed /tmp/tmph551oow1/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpttvnh9l5/f1.bed /tmp/tmpttvnh9l5/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpfb9bri9c/f1.bed /tmp/tmpfb9bri9c/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpeu4qytk4/f1.bed /tmp/tmpeu4qytk4/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp3ny0f74i/f1.bed /tmp/tmp3ny0f74i/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpmd0af5uc/f1.bed /tmp/tmpmd0af5uc/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpx46xjv0a/f1.bed /tmp/tmpx46xjv0a/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmptuc5u_ep/f1.bed /tmp/tmptuc5u_ep/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpip0kvjxw/f1.bed /tmp/tmpip0kvjxw/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpudqdzyt2/f1.bed /tmp/tmpudqdzyt2/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp8ptwlmku/f1.bed /tmp/tmp8ptwlmku/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp44z6331d/f1.bed /tmp/tmp44z6331d/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpfj0oh57e/f1.bed /tmp/tmpfj0oh57e/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpu4igaiqk/f1.bed /tmp/tmpu4igaiqk/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpkz9ju9rr/f1.bed /tmp/tmpkz9ju9rr/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp25j0hd8w/f1.bed /tmp/tmp25j0hd8w/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp7cam0_cx/f1.bed /tmp/tmp7cam0_cx/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpr6rpk6fm/f1.bed /tmp/tmpr6rpk6fm/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp_1huebg4/f1.bed /tmp/tmp_1huebg4/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp0ma8uzm4/f1.bed /tmp/tmp0ma8uzm4/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmptxzt8oif/f1.bed /tmp/tmptxzt8oif/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpjuhnvqul/f1.bed /tmp/tmpjuhnvqul/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpl94jsha7/f1.bed /tmp/tmpl94jsha7/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp23y5f2w7/f1.bed /tmp/tmp23y5f2w7/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpiiwmzzu3/f1.bed /tmp/tmpiiwmzzu3/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpbb226_k9/f1.bed /tmp/tmpbb226_k9/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpqtvynthx/f1.bed /tmp/tmpqtvynthx/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp4u6_lp1l/f1.bed /tmp/tmp4u6_lp1l/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpojc2ctvu/f1.bed /tmp/tmpojc2ctvu/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp1xs0eyu1/f1.bed /tmp/tmp1xs0eyu1/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp0ubrgsq7/f1.bed /tmp/tmp0ubrgsq7/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpyk34402m/f1.bed /tmp/tmpyk34402m/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmprdh9p_6l/f1.bed /tmp/tmprdh9p_6l/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp3wb_v4q0/f1.bed /tmp/tmp3wb_v4q0/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpkhatnykb/f1.bed /tmp/tmpkhatnykb/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpdcf74e9t/f1.bed /tmp/tmpdcf74e9t/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp2ispim24/f1.bed /tmp/tmp2ispim24/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpp8x8p74j/f1.bed /tmp/tmpp8x8p74j/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp_9rlwin_/f1.bed /tmp/tmp_9rlwin_/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpbqexb0te/f1.bed /tmp/tmpbqexb0te/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmptyf80dfg/f1.bed /tmp/tmptyf80dfg/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp5geiqf24/f1.bed /tmp/tmp5geiqf24/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpp74ov62p/f1.bed /tmp/tmpp74ov62p/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp_k0ucqyk/f1.bed /tmp/tmp_k0ucqyk/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpth8u_nxm/f1.bed /tmp/tmpth8u_nxm/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpyohsomis/f1.bed /tmp/tmpyohsomis/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpwvdddzvu/f1.bed /tmp/tmpwvdddzvu/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmptu7m2950/f1.bed /tmp/tmptu7m2950/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpoolmgn90/f1.bed /tmp/tmpoolmgn90/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp_4drap22/f1.bed /tmp/tmp_4drap22/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp4rchkrd2/f1.bed /tmp/tmp4rchkrd2/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp9s9og1z6/f1.bed /tmp/tmp9s9og1z6/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpvyg0suip/f1.bed /tmp/tmpvyg0suip/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpda1ntxq9/f1.bed /tmp/tmpda1ntxq9/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp78puey4h/f1.bed /tmp/tmp78puey4h/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpom3khq1e/f1.bed /tmp/tmpom3khq1e/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp8gxdv78l/f1.bed /tmp/tmp8gxdv78l/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpstf3_lor/f1.bed /tmp/tmpstf3_lor/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpa6lwe1rm/f1.bed /tmp/tmpa6lwe1rm/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp3og3vy9v/f1.bed /tmp/tmp3og3vy9v/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpa2o_klh0/f1.bed /tmp/tmpa2o_klh0/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpfietqsek/f1.bed /tmp/tmpfietqsek/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpgc9kxqm1/f1.bed /tmp/tmpgc9kxqm1/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpfz5pt5is/f1.bed /tmp/tmpfz5pt5is/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpbmlw1_ze/f1.bed /tmp/tmpbmlw1_ze/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpctd_x320/f1.bed /tmp/tmpctd_x320/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpzu9g84ux/f1.bed /tmp/tmpzu9g84ux/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpi3gwkj9y/f1.bed /tmp/tmpi3gwkj9y/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp86ozioau/f1.bed /tmp/tmp86ozioau/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpzfc950pg/f1.bed /tmp/tmpzfc950pg/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpxvflv029/f1.bed /tmp/tmpxvflv029/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp6zzxzo_e/f1.bed /tmp/tmp6zzxzo_e/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpbz9wntm1/f1.bed /tmp/tmpbz9wntm1/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp_9jdn449/f1.bed /tmp/tmp_9jdn449/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpatmt471f/f1.bed /tmp/tmpatmt471f/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp30jg9sqj/f1.bed /tmp/tmp30jg9sqj/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp57ns8mai/f1.bed /tmp/tmp57ns8mai/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpky5s_2q7/f1.bed /tmp/tmpky5s_2q7/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpqdh69qt5/f1.bed /tmp/tmpqdh69qt5/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp8c61lv_e/f1.bed /tmp/tmp8c61lv_e/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpyhrunaqd/f1.bed /tmp/tmpyhrunaqd/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmprhx_c58m/f1.bed /tmp/tmprhx_c58m/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp9am26ucc/f1.bed /tmp/tmp9am26ucc/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp2zmb887z/f1.bed /tmp/tmp2zmb887z/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp3zt2o32e/f1.bed /tmp/tmp3zt2o32e/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpj9b6xjbh/f1.bed /tmp/tmpj9b6xjbh/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp0gwg3bpf/f1.bed /tmp/tmp0gwg3bpf/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpnw_87cqf/f1.bed /tmp/tmpnw_87cqf/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpl3la56kn/f1.bed /tmp/tmpl3la56kn/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpzt24p56y/f1.bed /tmp/tmpzt24p56y/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp1u56qksb/f1.bed /tmp/tmp1u56qksb/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpmyjg6aai/f1.bed /tmp/tmpmyjg6aai/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpdvj9w8uq/f1.bed /tmp/tmpdvj9w8uq/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpf8lesg9o/f1.bed /tmp/tmpf8lesg9o/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpi36c2gam/f1.bed /tmp/tmpi36c2gam/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp2mii0vj_/f1.bed /tmp/tmp2mii0vj_/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp1gplb3ig/f1.bed /tmp/tmp1gplb3ig/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpmilnk3pt/f1.bed /tmp/tmpmilnk3pt/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpq0y2t_2n/f1.bed /tmp/tmpq0y2t_2n/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpymgt3uge/f1.bed /tmp/tmpymgt3uge/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpjfynu_pg/f1.bed /tmp/tmpjfynu_pg/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp8k0olnh7/f1.bed /tmp/tmp8k0olnh7/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpr4jmwft_/f1.bed /tmp/tmpr4jmwft_/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp7n5uqv20/f1.bed /tmp/tmp7n5uqv20/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpkk9rru__/f1.bed /tmp/tmpkk9rru__/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpz0polx2d/f1.bed /tmp/tmpz0polx2d/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpg7bgm20g/f1.bed /tmp/tmpg7bgm20g/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpe6e0v2ce/f1.bed /tmp/tmpe6e0v2ce/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp3oprbm8a/f1.bed /tmp/tmp3oprbm8a/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpvjqg60it/f1.bed /tmp/tmpvjqg60it/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp_3825_r4/f1.bed /tmp/tmp_3825_r4/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpc4ws8lk9/f1.bed /tmp/tmpc4ws8lk9/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpmm0ufea3/f1.bed /tmp/tmpmm0ufea3/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp8w3873k2/f1.bed /tmp/tmp8w3873k2/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpxhbco6t9/f1.bed /tmp/tmpxhbco6t9/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpdzd42xbf/f1.bed /tmp/tmpdzd42xbf/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp3gbq2msd/f1.bed /tmp/tmp3gbq2msd/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpfxiu8kgw/f1.bed /tmp/tmpfxiu8kgw/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpf2lpgwxh/f1.bed /tmp/tmpf2lpgwxh/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpi6jfaheo/f1.bed /tmp/tmpi6jfaheo/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpjfu2qmqw/f1.bed /tmp/tmpjfu2qmqw/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpzfk3mz3g/f1.bed /tmp/tmpzfk3mz3g/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp4hncr9sc/f1.bed /tmp/tmp4hncr9sc/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp32d6po86/f1.bed /tmp/tmp32d6po86/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpcnk4rfhs/f1.bed /tmp/tmpcnk4rfhs/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpvtpjwjk3/f1.bed /tmp/tmpvtpjwjk3/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpii7k4bb1/f1.bed /tmp/tmpii7k4bb1/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp0qraw28x/f1.bed /tmp/tmp0qraw28x/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmptbysgp80/f1.bed /tmp/tmptbysgp80/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpcwzi2jy0/f1.bed /tmp/tmpcwzi2jy0/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpqp2l97w6/f1.bed /tmp/tmpqp2l97w6/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp_rm6m299/f1.bed /tmp/tmp_rm6m299/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpeeuok4xr/f1.bed /tmp/tmpeeuok4xr/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpvyvyzw0a/f1.bed /tmp/tmpvyvyzw0a/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp4v4kyykt/f1.bed /tmp/tmp4v4kyykt/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmptkcjo43h/f1.bed /tmp/tmptkcjo43h/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp3uotb686/f1.bed /tmp/tmp3uotb686/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpj52yvls4/f1.bed /tmp/tmpj52yvls4/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp3n2sq68s/f1.bed /tmp/tmp3n2sq68s/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpvqi3y7nq/f1.bed /tmp/tmpvqi3y7nq/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpazhukkqz/f1.bed /tmp/tmpazhukkqz/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp5461uq6a/f1.bed /tmp/tmp5461uq6a/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpglcharo2/f1.bed /tmp/tmpglcharo2/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpxw5qu3dy/f1.bed /tmp/tmpxw5qu3dy/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmplcltgghc/f1.bed /tmp/tmplcltgghc/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpcaklbs2s/f1.bed /tmp/tmpcaklbs2s/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmps3wwsywf/f1.bed /tmp/tmps3wwsywf/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp9bkyy1t1/f1.bed /tmp/tmp9bkyy1t1/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp390k74b8/f1.bed /tmp/tmp390k74b8/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpafis1oph/f1.bed /tmp/tmpafis1oph/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp1q_8fmbn/f1.bed /tmp/tmp1q_8fmbn/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp_a_frlxu/f1.bed /tmp/tmp_a_frlxu/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpjoutrkqy/f1.bed /tmp/tmpjoutrkqy/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpz_hnq_p5/f1.bed /tmp/tmpz_hnq_p5/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp75qgi24n/f1.bed /tmp/tmp75qgi24n/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpcvpcim_q/f1.bed /tmp/tmpcvpcim_q/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmppr5fflwt/f1.bed /tmp/tmppr5fflwt/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpmyufoqnw/f1.bed /tmp/tmpmyufoqnw/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpzri9o87k/f1.bed /tmp/tmpzri9o87k/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpahj7vgcy/f1.bed /tmp/tmpahj7vgcy/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpndraas71/f1.bed /tmp/tmpndraas71/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpf582fw60/f1.bed /tmp/tmpf582fw60/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpf1witoyo/f1.bed /tmp/tmpf1witoyo/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpp6xsmah6/f1.bed /tmp/tmpp6xsmah6/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpvfmn0wdf/f1.bed /tmp/tmpvfmn0wdf/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpl11ogdr0/f1.bed /tmp/tmpl11ogdr0/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpl8lesfj4/f1.bed /tmp/tmpl8lesfj4/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpwd5iv1l6/f1.bed /tmp/tmpwd5iv1l6/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp55jusbl1/f1.bed /tmp/tmp55jusbl1/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpn2tw1ehu/f1.bed /tmp/tmpn2tw1ehu/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmptygd0lq3/f1.bed /tmp/tmptygd0lq3/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp0qm01sam/f1.bed /tmp/tmp0qm01sam/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpec93g8eh/f1.bed /tmp/tmpec93g8eh/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpvoba3oi4/f1.bed /tmp/tmpvoba3oi4/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpum72rucf/f1.bed /tmp/tmpum72rucf/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpxjd0mjyv/f1.bed /tmp/tmpxjd0mjyv/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpww_7gjtl/f1.bed /tmp/tmpww_7gjtl/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpyay934_z/f1.bed /tmp/tmpyay934_z/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmprl1u68ho/f1.bed /tmp/tmprl1u68ho/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpd0m6anq5/f1.bed /tmp/tmpd0m6anq5/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmppgrm6je5/f1.bed /tmp/tmppgrm6je5/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp8_7vvwfu/f1.bed /tmp/tmp8_7vvwfu/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpvs02e8az/f1.bed /tmp/tmpvs02e8az/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpfr0d5hwm/f1.bed /tmp/tmpfr0d5hwm/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp2xvg6y1k/f1.bed /tmp/tmp2xvg6y1k/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmptou7zcea/f1.bed /tmp/tmptou7zcea/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpczlv1j6i/f1.bed /tmp/tmpczlv1j6i/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpn2l6fvwd/f1.bed /tmp/tmpn2l6fvwd/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmplqajfhfi/f1.bed /tmp/tmplqajfhfi/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp_bge0vkr/f1.bed /tmp/tmp_bge0vkr/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpxlzhmsra/f1.bed /tmp/tmpxlzhmsra/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmplajhvf7u/f1.bed /tmp/tmplajhvf7u/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpp9c51dl9/f1.bed /tmp/tmpp9c51dl9/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpuymqia_t/f1.bed /tmp/tmpuymqia_t/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmphrn_qon8/f1.bed /tmp/tmphrn_qon8/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpzh2395rk/f1.bed /tmp/tmpzh2395rk/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmps_f508ax/f1.bed /tmp/tmps_f508ax/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpm4hikcjx/f1.bed /tmp/tmpm4hikcjx/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpz_00oc1n/f1.bed /tmp/tmpz_00oc1n/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpgdn95ez_/f1.bed /tmp/tmpgdn95ez_/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp88m3lg2m/f1.bed /tmp/tmp88m3lg2m/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpdn58qih_/f1.bed /tmp/tmpdn58qih_/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpx4eytrix/f1.bed /tmp/tmpx4eytrix/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpkxo365wh/f1.bed /tmp/tmpkxo365wh/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpvorcdb4r/f1.bed /tmp/tmpvorcdb4r/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpcasdlym5/f1.bed /tmp/tmpcasdlym5/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp5ny0lv_o/f1.bed /tmp/tmp5ny0lv_o/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp1726cbm5/f1.bed /tmp/tmp1726cbm5/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp0iydcvyg/f1.bed /tmp/tmp0iydcvyg/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp4nmhmqg6/f1.bed /tmp/tmp4nmhmqg6/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmptts22xh1/f1.bed /tmp/tmptts22xh1/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpuhp4uw5x/f1.bed /tmp/tmpuhp4uw5x/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp545xskze/f1.bed /tmp/tmp545xskze/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpealovihf/f1.bed /tmp/tmpealovihf/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp6g8mp3dm/f1.bed /tmp/tmp6g8mp3dm/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp957_ok7o/f1.bed /tmp/tmp957_ok7o/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpgx9zty6t/f1.bed /tmp/tmpgx9zty6t/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpfnjz4rys/f1.bed /tmp/tmpfnjz4rys/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmplzngaf61/f1.bed /tmp/tmplzngaf61/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpv2z7hges/f1.bed /tmp/tmpv2z7hges/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpfglsbrt9/f1.bed /tmp/tmpfglsbrt9/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpigcdy_k5/f1.bed /tmp/tmpigcdy_k5/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp8tl3wtcf/f1.bed /tmp/tmp8tl3wtcf/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp12rov9y1/f1.bed /tmp/tmp12rov9y1/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmplgbjpdwl/f1.bed /tmp/tmplgbjpdwl/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpsp0e929e/f1.bed /tmp/tmpsp0e929e/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp8w9e6k7g/f1.bed /tmp/tmp8w9e6k7g/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp_5ixlzeo/f1.bed /tmp/tmp_5ixlzeo/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpqg6emmdm/f1.bed /tmp/tmpqg6emmdm/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp79ldjqgz/f1.bed /tmp/tmp79ldjqgz/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpcojbu0zd/f1.bed /tmp/tmpcojbu0zd/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmptcvtqeip/f1.bed /tmp/tmptcvtqeip/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmponbazfrb/f1.bed /tmp/tmponbazfrb/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmppr8967lc/f1.bed /tmp/tmppr8967lc/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpnw1cqin8/f1.bed /tmp/tmpnw1cqin8/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpo7t8qfr1/f1.bed /tmp/tmpo7t8qfr1/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpj2_8_m26/f1.bed /tmp/tmpj2_8_m26/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp3eev7qq5/f1.bed /tmp/tmp3eev7qq5/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpig0rhame/f1.bed /tmp/tmpig0rhame/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpxai4d5zw/f1.bed /tmp/tmpxai4d5zw/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpc5t2lbwu/f1.bed /tmp/tmpc5t2lbwu/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp2zfn19qr/f1.bed /tmp/tmp2zfn19qr/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmplwyuxwhw/f1.bed /tmp/tmplwyuxwhw/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpbnnn2b34/f1.bed /tmp/tmpbnnn2b34/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpl14rbn9y/f1.bed /tmp/tmpl14rbn9y/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp2z2jin4d/f1.bed /tmp/tmp2z2jin4d/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmppjs7l35v/f1.bed /tmp/tmppjs7l35v/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpjlm3ljzx/f1.bed /tmp/tmpjlm3ljzx/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpulf_rrdn/f1.bed /tmp/tmpulf_rrdn/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp0ls01td3/f1.bed /tmp/tmp0ls01td3/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp1tri7_7t/f1.bed /tmp/tmp1tri7_7t/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp2rilsrzz/f1.bed /tmp/tmp2rilsrzz/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpd8gbppme/f1.bed /tmp/tmpd8gbppme/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp2bvhfusc/f1.bed /tmp/tmp2bvhfusc/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmply5njh__/f1.bed /tmp/tmply5njh__/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpxmv3mhoq/f1.bed /tmp/tmpxmv3mhoq/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmppscad9f9/f1.bed /tmp/tmppscad9f9/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmprr3q2yt7/f1.bed /tmp/tmprr3q2yt7/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpzru4wr9k/f1.bed /tmp/tmpzru4wr9k/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpf4ajauas/f1.bed /tmp/tmpf4ajauas/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp_madwzd2/f1.bed /tmp/tmp_madwzd2/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmphhci8050/f1.bed /tmp/tmphhci8050/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp6nftt56h/f1.bed /tmp/tmp6nftt56h/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpdo4dtex8/f1.bed /tmp/tmpdo4dtex8/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpvlvci6bj/f1.bed /tmp/tmpvlvci6bj/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpln0it_rn/f1.bed /tmp/tmpln0it_rn/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp8gusojjv/f1.bed /tmp/tmp8gusojjv/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmporp0dd0x/f1.bed /tmp/tmporp0dd0x/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpeqij94ft/f1.bed /tmp/tmpeqij94ft/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp861_ri5q/f1.bed /tmp/tmp861_ri5q/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp9z0g5xeg/f1.bed /tmp/tmp9z0g5xeg/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpb1z7zb36/f1.bed /tmp/tmpb1z7zb36/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpr_pd_gxz/f1.bed /tmp/tmpr_pd_gxz/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpz65ltwl5/f1.bed /tmp/tmpz65ltwl5/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpl9bu4_v6/f1.bed /tmp/tmpl9bu4_v6/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpdsbiefxa/f1.bed /tmp/tmpdsbiefxa/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpqy24w7vj/f1.bed /tmp/tmpqy24w7vj/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpf67g0mom/f1.bed /tmp/tmpf67g0mom/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp2uybgtqx/f1.bed /tmp/tmp2uybgtqx/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp8q4jc96x/f1.bed /tmp/tmp8q4jc96x/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpuq_sfuvm/f1.bed /tmp/tmpuq_sfuvm/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpsyikuo34/f1.bed /tmp/tmpsyikuo34/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpjdx0ltqz/f1.bed /tmp/tmpjdx0ltqz/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpx3478og7/f1.bed /tmp/tmpx3478og7/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpekl19ksm/f1.bed /tmp/tmpekl19ksm/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmplpr93moc/f1.bed /tmp/tmplpr93moc/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp3zglify3/f1.bed /tmp/tmp3zglify3/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpkcc09u8z/f1.bed /tmp/tmpkcc09u8z/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp0s76a5my/f1.bed /tmp/tmp0s76a5my/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpugcqverr/f1.bed /tmp/tmpugcqverr/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpszg1u4sq/f1.bed /tmp/tmpszg1u4sq/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpffhvf00u/f1.bed /tmp/tmpffhvf00u/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmph1napctq/f1.bed /tmp/tmph1napctq/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp3a569_ly/f1.bed /tmp/tmp3a569_ly/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpfjf9xsua/f1.bed /tmp/tmpfjf9xsua/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpin4ywlnn/f1.bed /tmp/tmpin4ywlnn/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmph39sw4t3/f1.bed /tmp/tmph39sw4t3/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpxsb_b_ak/f1.bed /tmp/tmpxsb_b_ak/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp9web5qyl/f1.bed /tmp/tmp9web5qyl/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp0wvkkv4p/f1.bed /tmp/tmp0wvkkv4p/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpfp1wkrt8/f1.bed /tmp/tmpfp1wkrt8/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp8kl0xivc/f1.bed /tmp/tmp8kl0xivc/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpfmrdin7q/f1.bed /tmp/tmpfmrdin7q/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpocc7bunn/f1.bed /tmp/tmpocc7bunn/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmppgaqpgf3/f1.bed /tmp/tmppgaqpgf3/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpvhsml26c/f1.bed /tmp/tmpvhsml26c/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmps_77dher/f1.bed /tmp/tmps_77dher/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpqpwg86kz/f1.bed /tmp/tmpqpwg86kz/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpwf8si7xq/f1.bed /tmp/tmpwf8si7xq/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpj3ert3nr/f1.bed /tmp/tmpj3ert3nr/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmppq30v9e0/f1.bed /tmp/tmppq30v9e0/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp2605_n1s/f1.bed /tmp/tmp2605_n1s/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpcu18hk75/f1.bed /tmp/tmpcu18hk75/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpyft2kj96/f1.bed /tmp/tmpyft2kj96/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpgqmhr1di/f1.bed /tmp/tmpgqmhr1di/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp_k5kxsqt/f1.bed /tmp/tmp_k5kxsqt/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp6g00710e/f1.bed /tmp/tmp6g00710e/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpmbll6x2w/f1.bed /tmp/tmpmbll6x2w/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp4n4am3xc/f1.bed /tmp/tmp4n4am3xc/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpiln_lbjr/f1.bed /tmp/tmpiln_lbjr/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmprple0kpb/f1.bed /tmp/tmprple0kpb/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmprmphrzzk/f1.bed /tmp/tmprmphrzzk/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpadalrjno/f1.bed /tmp/tmpadalrjno/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp5j41c04c/f1.bed /tmp/tmp5j41c04c/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - ___________ test_three_in_a_row[strandedness_chain37-method_chain37] ___________ [gw8] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', False), method_chain = ('subtract', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('subtract', 'overlap'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:30 E /usr/lib/python3/dist-packages/pandas/core/dtypes/missing.py:207 E (and 18 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ____________ test_three_in_a_row[strandedness_chain5-method_chain5] ____________ [gw5] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', False), method_chain = ('set_union', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('set_union', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/init.py:174 E (and 188 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2CsZmBgqFfnY2BgZMAEAB+RATI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ___________ test_three_in_a_row[strandedness_chain13-method_chain13] ___________ [gw7] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', False), method_chain = ('set_intersect', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('set_intersect', 'join'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 E /usr/lib/python3/dist-packages/pandas/core/array_algos/take.py:574 E /usr/lib/python3/dist-packages/pandas/core/common.py:143 E (and 62 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2CAA0YGLAAAADUAAg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ___________ test_three_in_a_row[strandedness_chain77-method_chain77] ___________ [gw4] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', 'same'), method_chain = ('intersect', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('intersect', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:17 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:21 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:37 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:54 E (and 73 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BAAEYUCgwAAD4AAw==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ___________ test_three_in_a_row[strandedness_chain50-method_chain50] ___________ [gw10] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', 'same') method_chain = ('set_union', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('set_union', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E (and 120 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2DkCXtSLCE/g5GBkQETAABBzQKM') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ___________ test_three_in_a_row[strandedness_chain62-method_chain62] ___________ [gw9] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', 'same'), method_chain = ('set_intersect', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('set_intersect', 'join'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 E /usr/lib/python3/dist-packages/pandas/core/array_algos/take.py:574 E (and 61 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2CAA0YGLAAAADUAAg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ________________ test_k_nearest[downstream-False-opposite-last] ________________ [gw3] linux -- Python 3.12.6 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 880, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 510, in test_k_nearest | @pytest.mark.explore | ^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1722, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 548, in test_k_nearest | result = gr.k_nearest( | ^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2450, in k_nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 180, in _nearest | df = __nearest(d1, d2, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 115, in nearest_previous | lidx, ridx, dist = nearest_previous_idx(d1, d2, d1.__k__.values, ties) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 28, in nearest_previous_idx | lidx, ridx_pos, dist = k_nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/k_nearest.pyx", line 28, in sorted_nearest.src.k_nearest.k_nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_k_nearest( | nearest_how='downstream', | overlap=False, | strandedness='opposite', | ties='last', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:14 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:15 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:160 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:171 | (and 39 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2QAA0YGOGBkxBBiAAAAngAG') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 548, in test_k_nearest | result = gr.k_nearest( | ^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2450, in k_nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 180, in _nearest | df = __nearest(d1, d2, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 140, in nearest_next | lidx, ridx, dist = nearest_next_idx(d1, d2, d1.__k__.values, ties) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 56, in nearest_next_idx | lidx, ridx_pos, dist = k_nearest_next_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/k_nearest.pyx", line 55, in sorted_nearest.src.k_nearest.k_nearest_next_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_k_nearest( | nearest_how='downstream', | overlap=False, | strandedness='opposite', | ties='last', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:160 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:171 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:41 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:42 | (and 40 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2QAA0YGBGDEEGIEAACLAAY=') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpf540oo73/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf540oo73/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4ofiwe67/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4ofiwe67/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp98khyjz2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp98khyjz2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpj22w8l38/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj22w8l38/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpn50i726k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn50i726k/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3ohflv41/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3ohflv41/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdfqtxot7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdfqtxot7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpb2j_7vm2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb2j_7vm2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpg7_bjpoo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg7_bjpoo/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5juc3ayh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5juc3ayh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp003yphdz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp003yphdz/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp__v_ttbp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp__v_ttbp/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6hr_7aof/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6hr_7aof/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0atjqe4c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0atjqe4c/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmptdkzl4iz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptdkzl4iz/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp24f8dw1t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp24f8dw1t/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmphxup5m7z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphxup5m7z/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpo0qmk7w8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo0qmk7w8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpogb5myhi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpogb5myhi/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpy4rny5rj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy4rny5rj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnv0b5uax/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnv0b5uax/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp53qfmndo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp53qfmndo/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp__qgj11i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp__qgj11i/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7hmrbuxi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7hmrbuxi/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3k0irh2z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3k0irh2z/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpt0cymqfy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt0cymqfy/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpd6a9t4k9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd6a9t4k9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpf1t86my9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf1t86my9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp61n2mv_f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp61n2mv_f/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmph4vzmw_u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph4vzmw_u/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2c7b866e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2c7b866e/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdacs3iyo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdacs3iyo/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmo8ux0qn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmo8ux0qn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2lh07aep/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2lh07aep/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjzdi4ymf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjzdi4ymf/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmps38ksmsy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps38ksmsy/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9gff_gly/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9gff_gly/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4w2xrwlz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4w2xrwlz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5hu1inzy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5hu1inzy/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4kfn_a26/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4kfn_a26/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqj492gbq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqj492gbq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmppseokh_8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppseokh_8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmplfnvq0f5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplfnvq0f5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdfru3b98/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdfru3b98/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4oxgghhe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4oxgghhe/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbkp785jw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbkp785jw/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvdm44djv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvdm44djv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmplaa6z_7w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplaa6z_7w/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6kyxjphm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6kyxjphm/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkcuej1ow/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkcuej1ow/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpk1knthzc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk1knthzc/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpd71tzbhg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd71tzbhg/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgewu50i4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgewu50i4/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0uvp36s8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0uvp36s8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpi35ek8eg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi35ek8eg/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp36ih8s8g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp36ih8s8g/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxopset3a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxopset3a/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp29yhr_4b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp29yhr_4b/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpa5s_qb6m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa5s_qb6m/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpucxx1tnd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpucxx1tnd/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpigovydmn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpigovydmn/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnn5ocz3b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnn5ocz3b/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1gop28g5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1gop28g5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmps6_h9qhq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps6_h9qhq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqcyea7k5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqcyea7k5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvb29z4wm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvb29z4wm/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuuc65i0y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuuc65i0y/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpiwuw1xup/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiwuw1xup/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp31l34rbv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp31l34rbv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpi5kibj_j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi5kibj_j/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcci2swc3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcci2swc3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpemanbz0w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpemanbz0w/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvc0a90gr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvc0a90gr/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpr2bdhy_d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr2bdhy_d/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuwsbcic6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuwsbcic6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmppg2q0wi3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppg2q0wi3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwihqn658/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwihqn658/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpd5m0cauq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd5m0cauq/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpetoc0oc8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpetoc0oc8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpohzcy3lj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpohzcy3lj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2d3yu8bk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2d3yu8bk/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2xc29h30/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2xc29h30/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpr86sowvb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr86sowvb/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3qrm3b9v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3qrm3b9v/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9zmt94ek/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9zmt94ek/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmplnxvfra8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplnxvfra8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmaor9jqy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmaor9jqy/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1m6ij1cm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1m6ij1cm/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpp8xsm_do/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp8xsm_do/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp50r24p4u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp50r24p4u/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpefm0wx6_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpefm0wx6_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbqydh_rh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbqydh_rh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpp4rin0fx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp4rin0fx/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3dzmp46l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3dzmp46l/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8vtsvjy2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8vtsvjy2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjuojag2w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjuojag2w/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbhmb9szw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbhmb9szw/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpe0t2mbzx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe0t2mbzx/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnouvtdgf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnouvtdgf/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1gpewmp6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1gpewmp6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxmfmvob8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxmfmvob8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0j4t38cf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0j4t38cf/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpat_11e9b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpat_11e9b/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpt62fjdba/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt62fjdba/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpd2a8xp13/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd2a8xp13/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpy0xyu36w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy0xyu36w/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6gkdrg5b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6gkdrg5b/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyytgvkux/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyytgvkux/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsr7kpz5d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsr7kpz5d/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp18pedz8s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp18pedz8s/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7hqqx4u1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7hqqx4u1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9yodfh70/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9yodfh70/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9m6ravlq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9m6ravlq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpd6mewv21/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd6mewv21/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmplnz8lh6t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplnz8lh6t/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpflizyas9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpflizyas9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyitwrfsc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyitwrfsc/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcxr230ij/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcxr230ij/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmph7_bxg8e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph7_bxg8e/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmplo5n8q8_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplo5n8q8_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpo5xq84ej/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo5xq84ej/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmprkd99d8y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprkd99d8y/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmppl17x0al/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppl17x0al/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmps_icvubk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps_icvubk/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3cliqrkd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3cliqrkd/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpp6k9zi4e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp6k9zi4e/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpydng94t1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpydng94t1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxglgzkz9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxglgzkz9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmps1300co6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps1300co6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmphhj8vzc8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphhj8vzc8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpa_h4f4ij/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa_h4f4ij/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqhqzzix_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqhqzzix_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmppzj4gii5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppzj4gii5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcz42zcw_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcz42zcw_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpk8sieyn0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk8sieyn0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuhy8mqiq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuhy8mqiq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfjsg3wv7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfjsg3wv7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp66vjhrgp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp66vjhrgp/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpj965niqs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj965niqs/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp05h7fzsh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp05h7fzsh/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6lhpvkw1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6lhpvkw1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwhx6bf0s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwhx6bf0s/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9a2sg28h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9a2sg28h/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp18ivwb1i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp18ivwb1i/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfdho7jll/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfdho7jll/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfcm77m2f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfcm77m2f/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9_9763ac/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9_9763ac/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpts_7lhxm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpts_7lhxm/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7r1uayxj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7r1uayxj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_opfuydk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_opfuydk/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwdl0xue1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwdl0xue1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4qmf614l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4qmf614l/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp47f_j171/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp47f_j171/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpk9vvjjo1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk9vvjjo1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3mtetg4k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3mtetg4k/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcp_qo0j4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcp_qo0j4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7gi722an/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7gi722an/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpckm1msjs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpckm1msjs/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7h6eys1a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7h6eys1a/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmphrkcy9hw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphrkcy9hw/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmph9kg7cm5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph9kg7cm5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbo4n7l45/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbo4n7l45/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmppfbsv_39/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppfbsv_39/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0wocxz01/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0wocxz01/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpba4dzzwo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpba4dzzwo/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpj6tf__cq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj6tf__cq/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9qngs7bn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9qngs7bn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpottaaya1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpottaaya1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpouk_28t6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpouk_28t6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbi03aobv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbi03aobv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpc7leq581/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc7leq581/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpi4h69d2w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi4h69d2w/f2.bed) ----------------------------- Captured stderr call ----------------------------- Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr6 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr8 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. ___________ test_three_in_a_row[strandedness_chain24-method_chain24] ___________ [gw6] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', False), method_chain = ('nearest', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:63: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('nearest', 'nearest'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:73 E (and 27 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2TABIw4OWAAAACXAAQ=') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +13 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1348862 | 1354449 | a | 0 | ... | | chr13 | 5144232 | 5147364 | a | 0 | ... | | chr13 | 2282917 | 2288100 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 18 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 13 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance, ... (+ 6 more.) ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ______________________ test_nearest[downstream-True-same] ______________________ [gw2] linux -- Python 3.12.6 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 880, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 323, in test_nearest | @pytest.mark.parametrize("nearest_how,overlap,strandedness", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1722, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 3 distinct failures. (3 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 351, in test_nearest | result = gr.nearest( | ^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 115, in _nearest | r_idx, dist = _next_nonoverlapping(df_to_find_nearest_in.End, | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 62, in _next_nonoverlapping | r_idx, dist = nearest_next_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 34, in sorted_nearest.src.sorted_nearest.nearest_next_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_nearest( | nearest_how='downstream', | overlap=True, | strandedness='same', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 4987907 | 4994006 | a | 0 | + | | | chr1 | 1429347 | 1431424 | a | 0 | - | | | chr1 | 1354433 | 1360532 | a | 0 | - | | | chr7 | 1531430 | 1537529 | a | 0 | + | | | chr15 | 2 | 4987 | a | 0 | - | | | chr17 | 6212588 | 6218687 | a | 0 | + | | | chr17 | 6349561 | 6355660 | a | 0 | + | | | chr17 | 9445392 | 9451491 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 8 rows and 6 columns from 4 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 9053 | a | 0 | + | | | chr1 | 3623440 | 3633174 | a | 0 | + | | | chr1 | 6231509 | 6238517 | a | 0 | + | | | chr1 | 6653796 | 6660657 | a | 0 | - | | | ... | ... | ... | ... | ... | ... | | | chr14 | 7005580 | 7011294 | a | 0 | + | | | chr14 | 238287 | 245295 | a | 0 | + | | | chr15 | 7693653 | 7700661 | a | 0 | + | | | chr19 | 2552805 | 2559813 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 11 rows and 6 columns from 5 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | (and 123 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'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') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 351, in test_nearest | result = gr.nearest( | ^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 118, in _nearest | r_idx, dist = _previous_nonoverlapping(df_to_find_nearest_in.Start, | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_nearest( | nearest_how='downstream', | overlap=True, | strandedness='same', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | (and 128 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2QAA0YGOGBkhIowIskwAgAAwAAJ') as a decorator on your test case +---------------- 3 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 359, in test_nearest | compare_results_nearest(bedtools_df, result) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 107, in compare_results_nearest | assert_df_equal(result_df, bedtools_df) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/helpers.py", line 60, in assert_df_equal | pd.testing.assert_frame_equal(df1, df2) | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 1279, in assert_frame_equal | assert_series_equal( | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 975, in assert_series_equal | assert_attr_equal("dtype", left, right, obj=f"Attributes of {obj}") | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 421, in assert_attr_equal | raise_assert_detail(obj, msg, left_attr, right_attr) | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 614, in raise_assert_detail | raise AssertionError(msg) | AssertionError: Attributes of DataFrame.iloc[:, 4] (column name="Distance") are different | | Attribute "dtype" are different | [left]: int32 | [right]: int64 | Falsifying example: test_nearest( | nearest_how='downstream', | overlap=True, | strandedness='same', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | (and 470 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2QAA0YGOGBkxBQCAACfAAc=') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5v8d89l4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5v8d89l4/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp19y0am7d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp19y0am7d/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_ygr_sey/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_ygr_sey/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 9053 + 0 1 chr1 2552805 2561104 - 0 2 chr1 3623440 3633174 + 0 3 chr1 6231509 6238517 + 0 4 chr1 6653796 6660657 - 0 5 chr1 9287220 9291791 - 0 6 chr12 6284801 6291809 + 0 7 chr14 238287 245295 + 0 8 chr14 7005580 7011294 + 0 9 chr15 7693653 7700661 + 0 10 chr19 2552805 2559813 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 9053 | a | 0 | ... | | chr1 | 3623440 | 3633174 | a | 0 | ... | | chr1 | 6231509 | 6238517 | a | 0 | ... | | chr1 | 6653796 | 6660657 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr14 | 7005580 | 7011294 | a | 0 | ... | | chr14 | 238287 | 245295 | a | 0 | ... | | chr15 | 7693653 | 7700661 | a | 0 | ... | | chr19 | 2552805 | 2559813 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 11 rows and 12 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 9053 + 0 8 chr14 238287 245295 + 0 10 chr19 2552805 2559813 + 0 5 chr1 2552805 2561104 - 0 1 chr1 3623440 3633174 + 0 2 chr1 6231509 6238517 + 0 6 chr12 6284801 6291809 + 0 3 chr1 6653796 6660657 - 0 7 chr14 7005580 7011294 + 0 9 chr15 7693653 7700661 + 0 4 chr1 9287220 9291791 - 0 df2 Chromosome Start End Strand Distance 0 chr1 2 9053 + 0 7 chr14 238287 245295 + 0 10 chr19 2552805 2559813 + 0 1 chr1 2552805 2561104 - 0 2 chr1 3623440 3633174 + 0 3 chr1 6231509 6238517 + 0 6 chr12 6284801 6291809 + 0 4 chr1 6653796 6660657 - 0 8 chr14 7005580 7011294 + 0 9 chr15 7693653 7700661 + 0 5 chr1 9287220 9291791 - 0 Actual Chromosome Start End Strand Distance 0 chr1 2 9053 + 0 1 chr1 2552805 2561104 - 0 2 chr1 3623440 3633174 + 0 3 chr1 6231509 6238517 + 0 4 chr1 6653796 6660657 - 0 5 chr1 9287220 9291791 - 0 6 chr12 6284801 6291809 + 0 7 chr14 238287 245295 + 0 8 chr14 7005580 7011294 + 0 9 chr15 7693653 7700661 + 0 10 chr19 2552805 2559813 + 0 Expected Chromosome Start End Strand Distance 0 chr1 2 9053 + 0 1 chr1 2552805 2561104 - 0 2 chr1 3623440 3633174 + 0 3 chr1 6231509 6238517 + 0 4 chr1 6653796 6660657 - 0 5 chr1 9287220 9291791 - 0 6 chr12 6284801 6291809 + 0 7 chr14 238287 245295 + 0 8 chr14 7005580 7011294 + 0 9 chr15 7693653 7700661 + 0 10 chr19 2552805 2559813 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=11, step=1) Expected index RangeIndex(start=0, stop=11, step=1) index equal [ True True True True True True True True True True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3oz6bc4w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3oz6bc4w/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpu8qonqjw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu8qonqjw/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 7 - 0 1 chr1 83 88 - 0 2 chr1 3623440 3623445 - 0 3 chr1 6231509 6231510 - 0 4 chr1 6653796 6653801 - 0 5 chr1 9287220 9287477 - 0 6 chr12 6284801 6284806 - 0 7 chr14 238287 238544 - 0 8 chr14 7005580 7005585 - 0 9 chr15 7693653 7693769 - 0 10 chr19 83 340 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 7 | a | 0 | ... | | chr1 | 6653796 | 6653801 | a | 0 | ... | | chr1 | 3623440 | 3623445 | a | 0 | ... | | chr1 | 6231509 | 6231510 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr14 | 7005580 | 7005585 | a | 0 | ... | | chr14 | 238287 | 238544 | a | 0 | ... | | chr15 | 7693653 | 7693769 | a | 0 | ... | | chr19 | 83 | 340 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 11 rows and 12 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 7 - 0 5 chr1 83 88 - 0 10 chr19 83 340 - 0 8 chr14 238287 238544 - 0 2 chr1 3623440 3623445 - 0 3 chr1 6231509 6231510 - 0 6 chr12 6284801 6284806 - 0 1 chr1 6653796 6653801 - 0 7 chr14 7005580 7005585 - 0 9 chr15 7693653 7693769 - 0 4 chr1 9287220 9287477 - 0 df2 Chromosome Start End Strand Distance 0 chr1 2 7 - 0 1 chr1 83 88 - 0 10 chr19 83 340 - 0 7 chr14 238287 238544 - 0 2 chr1 3623440 3623445 - 0 3 chr1 6231509 6231510 - 0 6 chr12 6284801 6284806 - 0 4 chr1 6653796 6653801 - 0 8 chr14 7005580 7005585 - 0 9 chr15 7693653 7693769 - 0 5 chr1 9287220 9287477 - 0 Actual Chromosome Start End Strand Distance 0 chr1 2 7 - 0 1 chr1 83 88 - 0 2 chr1 3623440 3623445 - 0 3 chr1 6231509 6231510 - 0 4 chr1 6653796 6653801 - 0 5 chr1 9287220 9287477 - 0 6 chr12 6284801 6284806 - 0 7 chr14 238287 238544 - 0 8 chr14 7005580 7005585 - 0 9 chr15 7693653 7693769 - 0 10 chr19 83 340 - 0 Expected Chromosome Start End Strand Distance 0 chr1 2 7 - 0 1 chr1 83 88 - 0 2 chr1 3623440 3623445 - 0 3 chr1 6231509 6231510 - 0 4 chr1 6653796 6653801 - 0 5 chr1 9287220 9287477 - 0 6 chr12 6284801 6284806 - 0 7 chr14 238287 238544 - 0 8 chr14 7005580 7005585 - 0 9 chr15 7693653 7693769 - 0 10 chr19 83 340 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=11, step=1) Expected index RangeIndex(start=0, stop=11, step=1) index equal [ True True True True True True True True True True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9unkkhle/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9unkkhle/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpeqjhenst/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpeqjhenst/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4j5eyuo5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4j5eyuo5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwpix3o0d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwpix3o0d/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpz9hyx830/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz9hyx830/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6pf4uksw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6pf4uksw/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmz8ms82a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmz8ms82a/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpehrqz508/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpehrqz508/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzepv6cnc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzepv6cnc/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsup1l4gh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsup1l4gh/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8gsqkrm6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8gsqkrm6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplw8odx7z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplw8odx7z/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4dpsbf9t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4dpsbf9t/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxzi35odc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxzi35odc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptuci3qe0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptuci3qe0/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0eyiugo_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0eyiugo_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_z0cs17j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_z0cs17j/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprv3ksmlx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprv3ksmlx/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpa2q13yk1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa2q13yk1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgc4mb65n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgc4mb65n/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9iag2aoz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9iag2aoz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxsa8ufev/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxsa8ufev/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 8 17 - 0 1 chr1 8 91 - 0 2 chr1 8 91 - 0 3 chr1 65537 65538 - 0 4 chr1 65537 65620 - 0 5 chr1 65537 65620 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 65620 | a | 0 | ... | | chr1 | 8 | 91 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | | chr1 | 8 | 17 | a | 0 | ... | | chr1 | 65537 | 65620 | a | 0 | ... | | chr1 | 8 | 91 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 3 chr1 8 17 - 0 1 chr1 8 91 - 0 5 chr1 8 91 - 0 2 chr1 65537 65538 - 0 0 chr1 65537 65620 - 0 4 chr1 65537 65620 - 0 df2 Chromosome Start End Strand Distance 0 chr1 8 17 - 0 1 chr1 8 91 - 0 2 chr1 8 91 - 0 3 chr1 65537 65538 - 0 4 chr1 65537 65620 - 0 5 chr1 65537 65620 - 0 Actual Chromosome Start End Strand Distance 0 chr1 8 17 - 0 1 chr1 8 91 - 0 2 chr1 8 91 - 0 3 chr1 65537 65538 - 0 4 chr1 65537 65620 - 0 5 chr1 65537 65620 - 0 Expected Chromosome Start End Strand Distance 0 chr1 8 17 - 0 1 chr1 8 91 - 0 2 chr1 8 91 - 0 3 chr1 65537 65538 - 0 4 chr1 65537 65620 - 0 5 chr1 65537 65620 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppi2wyttg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppi2wyttg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzgy3gxks/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzgy3gxks/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpw3w0nw85/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw3w0nw85/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsxe2xfyu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsxe2xfyu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpy6gny1j8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy6gny1j8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_yd9fbfl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_yd9fbfl/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp62dbtqqe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp62dbtqqe/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpm0htgew7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm0htgew7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprgq5guax/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprgq5guax/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 4 - 0 1 chr1 1 4 - 0 2 chr1 1 4 - 0 3 chr1 1 4 - 0 4 chr1 1 4 - 0 5 chr1 1 4 - 0 6 chr1 1 4 - 0 7 chr1 1 4 - 0 8 chr1 1 4 - 0 9 chr1 1 4 - 0 10 chr1 1 4 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 4 | a | 0 | ... | | chr1 | 1 | 4 | a | 0 | ... | | chr1 | 1 | 4 | a | 0 | ... | | chr1 | 1 | 4 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 1 | 4 | a | 0 | ... | | chr1 | 1 | 4 | a | 0 | ... | | chr1 | 1 | 4 | a | 0 | ... | | chr1 | 1 | 4 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 11 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 4 - 0 1 chr1 1 4 - 0 2 chr1 1 4 - 0 3 chr1 1 4 - 0 4 chr1 1 4 - 0 5 chr1 1 4 - 0 6 chr1 1 4 - 0 7 chr1 1 4 - 0 8 chr1 1 4 - 0 9 chr1 1 4 - 0 10 chr1 1 4 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 4 - 0 1 chr1 1 4 - 0 2 chr1 1 4 - 0 3 chr1 1 4 - 0 4 chr1 1 4 - 0 5 chr1 1 4 - 0 6 chr1 1 4 - 0 7 chr1 1 4 - 0 8 chr1 1 4 - 0 9 chr1 1 4 - 0 10 chr1 1 4 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 4 - 0 1 chr1 1 4 - 0 2 chr1 1 4 - 0 3 chr1 1 4 - 0 4 chr1 1 4 - 0 5 chr1 1 4 - 0 6 chr1 1 4 - 0 7 chr1 1 4 - 0 8 chr1 1 4 - 0 9 chr1 1 4 - 0 10 chr1 1 4 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 4 - 0 1 chr1 1 4 - 0 2 chr1 1 4 - 0 3 chr1 1 4 - 0 4 chr1 1 4 - 0 5 chr1 1 4 - 0 6 chr1 1 4 - 0 7 chr1 1 4 - 0 8 chr1 1 4 - 0 9 chr1 1 4 - 0 10 chr1 1 4 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=11, step=1) Expected index RangeIndex(start=0, stop=11, step=1) index equal [ True True True True True True True True True True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsmtrk9fa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsmtrk9fa/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4 5 - 0 1 chr1 4 7 - 0 2 chr1 4 7 - 0 3 chr1 4 7 - 0 4 chr1 4 7 - 0 5 chr1 4 7 - 0 6 chr1 4 7 - 0 7 chr1 4 7 - 0 8 chr1 4 7 - 0 9 chr1 4 7 - 0 10 chr1 4 7 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4 | 7 | a | 0 | ... | | chr1 | 4 | 7 | a | 0 | ... | | chr1 | 4 | 7 | a | 0 | ... | | chr1 | 4 | 7 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 4 | 7 | a | 0 | ... | | chr1 | 4 | 7 | a | 0 | ... | | chr1 | 4 | 7 | a | 0 | ... | | chr1 | 4 | 5 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 11 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 10 chr1 4 5 - 0 0 chr1 4 7 - 0 1 chr1 4 7 - 0 2 chr1 4 7 - 0 3 chr1 4 7 - 0 4 chr1 4 7 - 0 5 chr1 4 7 - 0 6 chr1 4 7 - 0 7 chr1 4 7 - 0 8 chr1 4 7 - 0 9 chr1 4 7 - 0 df2 Chromosome Start End Strand Distance 0 chr1 4 5 - 0 1 chr1 4 7 - 0 2 chr1 4 7 - 0 3 chr1 4 7 - 0 4 chr1 4 7 - 0 5 chr1 4 7 - 0 6 chr1 4 7 - 0 7 chr1 4 7 - 0 8 chr1 4 7 - 0 9 chr1 4 7 - 0 10 chr1 4 7 - 0 Actual Chromosome Start End Strand Distance 0 chr1 4 5 - 0 1 chr1 4 7 - 0 2 chr1 4 7 - 0 3 chr1 4 7 - 0 4 chr1 4 7 - 0 5 chr1 4 7 - 0 6 chr1 4 7 - 0 7 chr1 4 7 - 0 8 chr1 4 7 - 0 9 chr1 4 7 - 0 10 chr1 4 7 - 0 Expected Chromosome Start End Strand Distance 0 chr1 4 5 - 0 1 chr1 4 7 - 0 2 chr1 4 7 - 0 3 chr1 4 7 - 0 4 chr1 4 7 - 0 5 chr1 4 7 - 0 6 chr1 4 7 - 0 7 chr1 4 7 - 0 8 chr1 4 7 - 0 9 chr1 4 7 - 0 10 chr1 4 7 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=11, step=1) Expected index RangeIndex(start=0, stop=11, step=1) index equal [ True True True True True True True True True True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpym8im_t8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpym8im_t8/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4 5 - 0 1 chr1 4 7 - 0 2 chr1 4 7 - 0 3 chr1 4 7 - 0 4 chr1 4 7 - 0 5 chr1 4 7 - 0 6 chr1 4 7 - 0 7 chr1 4 7 - 0 8 chr1 4 7 - 0 9 chr1 4 7 - 0 10 chr1 4 7 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4 | 7 | a | 0 | ... | | chr1 | 4 | 7 | a | 0 | ... | | chr1 | 4 | 7 | a | 0 | ... | | chr1 | 4 | 7 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 4 | 7 | a | 0 | ... | | chr1 | 4 | 7 | a | 0 | ... | | chr1 | 4 | 7 | a | 0 | ... | | chr1 | 4 | 5 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 11 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 10 chr1 4 5 - 0 0 chr1 4 7 - 0 1 chr1 4 7 - 0 2 chr1 4 7 - 0 3 chr1 4 7 - 0 4 chr1 4 7 - 0 5 chr1 4 7 - 0 6 chr1 4 7 - 0 7 chr1 4 7 - 0 8 chr1 4 7 - 0 9 chr1 4 7 - 0 df2 Chromosome Start End Strand Distance 0 chr1 4 5 - 0 1 chr1 4 7 - 0 2 chr1 4 7 - 0 3 chr1 4 7 - 0 4 chr1 4 7 - 0 5 chr1 4 7 - 0 6 chr1 4 7 - 0 7 chr1 4 7 - 0 8 chr1 4 7 - 0 9 chr1 4 7 - 0 10 chr1 4 7 - 0 Actual Chromosome Start End Strand Distance 0 chr1 4 5 - 0 1 chr1 4 7 - 0 2 chr1 4 7 - 0 3 chr1 4 7 - 0 4 chr1 4 7 - 0 5 chr1 4 7 - 0 6 chr1 4 7 - 0 7 chr1 4 7 - 0 8 chr1 4 7 - 0 9 chr1 4 7 - 0 10 chr1 4 7 - 0 Expected Chromosome Start End Strand Distance 0 chr1 4 5 - 0 1 chr1 4 7 - 0 2 chr1 4 7 - 0 3 chr1 4 7 - 0 4 chr1 4 7 - 0 5 chr1 4 7 - 0 6 chr1 4 7 - 0 7 chr1 4 7 - 0 8 chr1 4 7 - 0 9 chr1 4 7 - 0 10 chr1 4 7 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=11, step=1) Expected index RangeIndex(start=0, stop=11, step=1) index equal [ True True True True True True True True True True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpr3uo03p9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr3uo03p9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpus9byjga/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpus9byjga/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpy7j3aot2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy7j3aot2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwe22477q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwe22477q/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6dspo1n0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6dspo1n0/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmuihjw60/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmuihjw60/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3hpvcshw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3hpvcshw/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2s4pg6iz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2s4pg6iz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpc3__4no4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc3__4no4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpupvle9q2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpupvle9q2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptgg56g_j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptgg56g_j/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppwkev_ee/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppwkev_ee/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvjwb_o8s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvjwb_o8s/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4_9_kptw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4_9_kptw/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpncayz3m0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpncayz3m0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpoy_w7e1g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoy_w7e1g/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpv04ashnv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv04ashnv/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmparebd4e9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmparebd4e9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7qnifhp9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7qnifhp9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpakjo4bx5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpakjo4bx5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkxfr_dmk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkxfr_dmk/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_xp68r_t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_xp68r_t/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpghdstr_h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpghdstr_h/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmk7ps1nt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmk7ps1nt/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppz529sr_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppz529sr_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe7j6g5lo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe7j6g5lo/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe091zsxy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe091zsxy/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1di8mbss/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1di8mbss/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdnbmgc1_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdnbmgc1_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8gz17oy6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8gz17oy6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqgcja14y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqgcja14y/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3wmqpdjq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3wmqpdjq/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpg6_ecmas/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg6_ecmas/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqvqoq3m4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqvqoq3m4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5w7b747a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5w7b747a/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqyvfhbxw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqyvfhbxw/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppi4eceni/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppi4eceni/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmph47y03ms/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph47y03ms/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjtcvm665/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjtcvm665/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp41o8gwwx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp41o8gwwx/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8wqc43m0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8wqc43m0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmph8nth55h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph8nth55h/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphf6pi6qa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphf6pi6qa/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2uljfhm5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2uljfhm5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpoqgnk5_t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoqgnk5_t/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbe83ozyl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbe83ozyl/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplqmusaog/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplqmusaog/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpq57gw03u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq57gw03u/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp31hwv6gb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp31hwv6gb/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpi4tr0z_k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi4tr0z_k/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfquvjkj3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfquvjkj3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6wjgj4ox/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6wjgj4ox/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvg_74pap/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvg_74pap/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp95r76xz1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp95r76xz1/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmgg1w8iv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmgg1w8iv/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpksi9dwax/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpksi9dwax/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 3 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 3 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 3 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 3 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 3 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpw1ovy1vc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw1ovy1vc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxhdg9e2u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxhdg9e2u/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpf102ltk7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf102ltk7/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqxhov1nz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqxhov1nz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwo699bv4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwo699bv4/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprfpivpll/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprfpivpll/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsh6kk_oy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsh6kk_oy/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphjwjibz1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphjwjibz1/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5jra7jkv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5jra7jkv/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp406mmpu9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp406mmpu9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfo68r0kk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfo68r0kk/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbz0l8j4x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbz0l8j4x/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpay54hcp8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpay54hcp8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2lq9yuk3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2lq9yuk3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxjbfz_d6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxjbfz_d6/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9scmyrlh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9scmyrlh/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpygcbuqwr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpygcbuqwr/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe0og8s47/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe0og8s47/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpw3qxobjz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw3qxobjz/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpctgxpuwq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpctgxpuwq/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpi97ormke/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi97ormke/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpj2mc77pq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj2mc77pq/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5szbg29g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5szbg29g/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzjfdjk3r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzjfdjk3r/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuauq1e3a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuauq1e3a/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvb034axz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvb034axz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpazyia3w9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpazyia3w9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpi0hpj51b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi0hpj51b/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpv3fbbdfh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv3fbbdfh/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbxb101su/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbxb101su/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp027bagw0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp027bagw0/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain51-method_chain51] ___________ [gw10] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', 'same'), method_chain = ('set_union', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('set_union', 'overlap'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E (and 184 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2CAA0YGLAAAADUAAg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ___________________________ test_subtraction[False] ____________________________ [gw1] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness = False @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness", ["same", "opposite", False]) # tests/test_binary.py:286: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:308: in test_subtraction result = gr.subtract(gr2, strandedness=strandedness) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_subtraction( E strandedness=False, E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., # or any other generated value E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., # or any other generated value E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2TABIxYxAAAZAAD') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp5k6hcho4/f1.bed -b /tmp/tmp5k6hcho4/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp4z7kq89y/f1.bed -b /tmp/tmp4z7kq89y/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpmq0wa8q2/f1.bed -b /tmp/tmpmq0wa8q2/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp2zlwamec/f1.bed -b /tmp/tmp2zlwamec/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpkwe24pv2/f1.bed -b /tmp/tmpkwe24pv2/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmprc6mr1hz/f1.bed -b /tmp/tmprc6mr1hz/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpakmekn7p/f1.bed -b /tmp/tmpakmekn7p/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp5vtlh1d6/f1.bed -b /tmp/tmp5vtlh1d6/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp3j264u_n/f1.bed -b /tmp/tmp3j264u_n/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp7i2v8ssr/f1.bed -b /tmp/tmp7i2v8ssr/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp348xrivm/f1.bed -b /tmp/tmp348xrivm/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpjr8yakra/f1.bed -b /tmp/tmpjr8yakra/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpqu2amc6v/f1.bed -b /tmp/tmpqu2amc6v/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp4va3md6p/f1.bed -b /tmp/tmp4va3md6p/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpig0rnva8/f1.bed -b /tmp/tmpig0rnva8/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp94izxd1y/f1.bed -b /tmp/tmp94izxd1y/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpdjhstgbt/f1.bed -b /tmp/tmpdjhstgbt/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpsv27we_3/f1.bed -b /tmp/tmpsv27we_3/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpg5t87skw/f1.bed -b /tmp/tmpg5t87skw/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp3m7w_1ll/f1.bed -b /tmp/tmp3m7w_1ll/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpwt3qmavr/f1.bed -b /tmp/tmpwt3qmavr/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpuww_m_39/f1.bed -b /tmp/tmpuww_m_39/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp89iq5pzo/f1.bed -b /tmp/tmp89iq5pzo/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpllui88dn/f1.bed -b /tmp/tmpllui88dn/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpn89k8emu/f1.bed -b /tmp/tmpn89k8emu/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpas562zr9/f1.bed -b /tmp/tmpas562zr9/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpju62p_hm/f1.bed -b /tmp/tmpju62p_hm/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpk62p_h6u/f1.bed -b /tmp/tmpk62p_h6u/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpe9x1g4vq/f1.bed -b /tmp/tmpe9x1g4vq/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmphfu57i0c/f1.bed -b /tmp/tmphfu57i0c/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpbyldmoc0/f1.bed -b /tmp/tmpbyldmoc0/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpg0wso154/f1.bed -b /tmp/tmpg0wso154/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpfzxlkve4/f1.bed -b /tmp/tmpfzxlkve4/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp3e3gza5a/f1.bed -b /tmp/tmp3e3gza5a/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpbg10f3af/f1.bed -b /tmp/tmpbg10f3af/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp_6sohim7/f1.bed -b /tmp/tmp_6sohim7/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpedzm42p5/f1.bed -b /tmp/tmpedzm42p5/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpg29tgn7x/f1.bed -b /tmp/tmpg29tgn7x/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpnw6s6yqn/f1.bed -b /tmp/tmpnw6s6yqn/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpys98ci9m/f1.bed -b /tmp/tmpys98ci9m/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp0_ady0kv/f1.bed -b /tmp/tmp0_ady0kv/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpiomv1_qd/f1.bed -b /tmp/tmpiomv1_qd/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp14xs41uh/f1.bed -b /tmp/tmp14xs41uh/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp7hd34gqg/f1.bed -b /tmp/tmp7hd34gqg/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp_s9t5auv/f1.bed -b /tmp/tmp_s9t5auv/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpjti9z3qw/f1.bed -b /tmp/tmpjti9z3qw/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpp7ngc_i9/f1.bed -b /tmp/tmpp7ngc_i9/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpa47qrur9/f1.bed -b /tmp/tmpa47qrur9/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpw1ea1eyk/f1.bed -b /tmp/tmpw1ea1eyk/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpn4zii8hj/f1.bed -b /tmp/tmpn4zii8hj/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpdbrui92a/f1.bed -b /tmp/tmpdbrui92a/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpte784yhc/f1.bed -b /tmp/tmpte784yhc/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpnyn67lfu/f1.bed -b /tmp/tmpnyn67lfu/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmps5miz1oc/f1.bed -b /tmp/tmps5miz1oc/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpjin1ve_s/f1.bed -b /tmp/tmpjin1ve_s/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp0z330o74/f1.bed -b /tmp/tmp0z330o74/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp4qbfe7rd/f1.bed -b /tmp/tmp4qbfe7rd/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp8kdxlnjb/f1.bed -b /tmp/tmp8kdxlnjb/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpnzbnj81k/f1.bed -b /tmp/tmpnzbnj81k/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpclrj3t41/f1.bed -b /tmp/tmpclrj3t41/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp1_3nhr8e/f1.bed -b /tmp/tmp1_3nhr8e/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpz6m0ju31/f1.bed -b /tmp/tmpz6m0ju31/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpef4h4lt4/f1.bed -b /tmp/tmpef4h4lt4/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp40csuqf0/f1.bed -b /tmp/tmp40csuqf0/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpom8e2kdq/f1.bed -b /tmp/tmpom8e2kdq/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp73k1del2/f1.bed -b /tmp/tmp73k1del2/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp7dqvb9r0/f1.bed -b /tmp/tmp7dqvb9r0/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpsjpogeqh/f1.bed -b /tmp/tmpsjpogeqh/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpwecndmxh/f1.bed -b /tmp/tmpwecndmxh/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpr0tlhf06/f1.bed -b /tmp/tmpr0tlhf06/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpwe1l_ci7/f1.bed -b /tmp/tmpwe1l_ci7/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpwzfklxxb/f1.bed -b /tmp/tmpwzfklxxb/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpy5od2vi3/f1.bed -b /tmp/tmpy5od2vi3/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmprtrgiqbn/f1.bed -b /tmp/tmprtrgiqbn/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpyzgx4ff3/f1.bed -b /tmp/tmpyzgx4ff3/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpt75o87ls/f1.bed -b /tmp/tmpt75o87ls/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpspn4bglv/f1.bed -b /tmp/tmpspn4bglv/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpe7xtnq59/f1.bed -b /tmp/tmpe7xtnq59/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpi12l_tis/f1.bed -b /tmp/tmpi12l_tis/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpvaqyej70/f1.bed -b /tmp/tmpvaqyej70/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmprly5i15k/f1.bed -b /tmp/tmprly5i15k/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp59t6cxwo/f1.bed -b /tmp/tmp59t6cxwo/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpui_hshnp/f1.bed -b /tmp/tmpui_hshnp/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpem1_erj1/f1.bed -b /tmp/tmpem1_erj1/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp2lfgb21p/f1.bed -b /tmp/tmp2lfgb21p/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpdi9lwhfw/f1.bed -b /tmp/tmpdi9lwhfw/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp2dnwkuc4/f1.bed -b /tmp/tmp2dnwkuc4/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpci14lftx/f1.bed -b /tmp/tmpci14lftx/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpfewkvgs3/f1.bed -b /tmp/tmpfewkvgs3/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp7vg5_7jp/f1.bed -b /tmp/tmp7vg5_7jp/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpe6fke0td/f1.bed -b /tmp/tmpe6fke0td/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmph4w1m6kk/f1.bed -b /tmp/tmph4w1m6kk/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp1jaw7nz3/f1.bed -b /tmp/tmp1jaw7nz3/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp4y6jijzj/f1.bed -b /tmp/tmp4y6jijzj/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpd21h14_r/f1.bed -b /tmp/tmpd21h14_r/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpi9m51kze/f1.bed -b /tmp/tmpi9m51kze/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpyrtlzmdb/f1.bed -b /tmp/tmpyrtlzmdb/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp3d2jy7_f/f1.bed -b /tmp/tmp3d2jy7_f/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpniskem07/f1.bed -b /tmp/tmpniskem07/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpa1y9rh9r/f1.bed -b /tmp/tmpa1y9rh9r/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmptaya4gmq/f1.bed -b /tmp/tmptaya4gmq/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpt4n3jgmw/f1.bed -b /tmp/tmpt4n3jgmw/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp5dj3mkgg/f1.bed -b /tmp/tmp5dj3mkgg/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp3xny59ga/f1.bed -b /tmp/tmp3xny59ga/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpjekpmoo2/f1.bed -b /tmp/tmpjekpmoo2/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp0cozhi8y/f1.bed -b /tmp/tmp0cozhi8y/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpnbh5eli6/f1.bed -b /tmp/tmpnbh5eli6/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmph6rw5nbj/f1.bed -b /tmp/tmph6rw5nbj/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpw74u1etc/f1.bed -b /tmp/tmpw74u1etc/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpgbi7rbk_/f1.bed -b /tmp/tmpgbi7rbk_/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmplnxh2sd1/f1.bed -b /tmp/tmplnxh2sd1/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp8elx3jjd/f1.bed -b /tmp/tmp8elx3jjd/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpk4c560qw/f1.bed -b /tmp/tmpk4c560qw/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmphcc5cfoz/f1.bed -b /tmp/tmphcc5cfoz/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpu6scberk/f1.bed -b /tmp/tmpu6scberk/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp67ju04h8/f1.bed -b /tmp/tmp67ju04h8/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp4iy8ye5w/f1.bed -b /tmp/tmp4iy8ye5w/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpashqwy3v/f1.bed -b /tmp/tmpashqwy3v/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp_zh9_cpj/f1.bed -b /tmp/tmp_zh9_cpj/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpvqcw8ka5/f1.bed -b /tmp/tmpvqcw8ka5/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp0nmirl9g/f1.bed -b /tmp/tmp0nmirl9g/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpmodr3fgu/f1.bed -b /tmp/tmpmodr3fgu/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpmq25ksq_/f1.bed -b /tmp/tmpmq25ksq_/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpqy0h35jp/f1.bed -b /tmp/tmpqy0h35jp/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpxqatky39/f1.bed -b /tmp/tmpxqatky39/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpc894pbh3/f1.bed -b /tmp/tmpc894pbh3/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpwpmfzsdb/f1.bed -b /tmp/tmpwpmfzsdb/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpzac7k3h0/f1.bed -b /tmp/tmpzac7k3h0/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpcfzf51ob/f1.bed -b /tmp/tmpcfzf51ob/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpub26be4z/f1.bed -b /tmp/tmpub26be4z/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp3h7ojouq/f1.bed -b /tmp/tmp3h7ojouq/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpxyntg1bj/f1.bed -b /tmp/tmpxyntg1bj/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpfwdvhwq6/f1.bed -b /tmp/tmpfwdvhwq6/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpxr_zu7xy/f1.bed -b /tmp/tmpxr_zu7xy/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpuws8__r0/f1.bed -b /tmp/tmpuws8__r0/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp0v405pwt/f1.bed -b /tmp/tmp0v405pwt/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpkz743unf/f1.bed -b /tmp/tmpkz743unf/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpxnl0eqsg/f1.bed -b /tmp/tmpxnl0eqsg/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp8wl2q44d/f1.bed -b /tmp/tmp8wl2q44d/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpwrzxt7oa/f1.bed -b /tmp/tmpwrzxt7oa/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpwny253uk/f1.bed -b /tmp/tmpwny253uk/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpbr_irti1/f1.bed -b /tmp/tmpbr_irti1/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp22u53dm1/f1.bed -b /tmp/tmp22u53dm1/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmppe0dyud_/f1.bed -b /tmp/tmppe0dyud_/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp2kau722r/f1.bed -b /tmp/tmp2kau722r/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpb3se3vv3/f1.bed -b /tmp/tmpb3se3vv3/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpbfict_jv/f1.bed -b /tmp/tmpbfict_jv/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp7230kdki/f1.bed -b /tmp/tmp7230kdki/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpk_sif8rv/f1.bed -b /tmp/tmpk_sif8rv/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpsk6ctu0s/f1.bed -b /tmp/tmpsk6ctu0s/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp_cu1zxzq/f1.bed -b /tmp/tmp_cu1zxzq/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpe_vz2vj9/f1.bed -b /tmp/tmpe_vz2vj9/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp25mcwdqx/f1.bed -b /tmp/tmp25mcwdqx/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpnzz72dyy/f1.bed -b /tmp/tmpnzz72dyy/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpgxb3g115/f1.bed -b /tmp/tmpgxb3g115/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpzuu8h3o2/f1.bed -b /tmp/tmpzuu8h3o2/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpv4qx2ips/f1.bed -b /tmp/tmpv4qx2ips/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpa9t7zx6r/f1.bed -b /tmp/tmpa9t7zx6r/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpdlqylk_5/f1.bed -b /tmp/tmpdlqylk_5/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpekzbwh5d/f1.bed -b /tmp/tmpekzbwh5d/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpsw6aqte0/f1.bed -b /tmp/tmpsw6aqte0/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp4lum7yng/f1.bed -b /tmp/tmp4lum7yng/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp_hkrqsnf/f1.bed -b /tmp/tmp_hkrqsnf/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp2lx0pmvt/f1.bed -b /tmp/tmp2lx0pmvt/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpv_obn09l/f1.bed -b /tmp/tmpv_obn09l/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpgmrb15kt/f1.bed -b /tmp/tmpgmrb15kt/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp5saud4_u/f1.bed -b /tmp/tmp5saud4_u/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp7ru86ejf/f1.bed -b /tmp/tmp7ru86ejf/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpvr4gmw2h/f1.bed -b /tmp/tmpvr4gmw2h/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp7872nbmi/f1.bed -b /tmp/tmp7872nbmi/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpsp7xj_hi/f1.bed -b /tmp/tmpsp7xj_hi/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpjfpesqw4/f1.bed -b /tmp/tmpjfpesqw4/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp1ex4hxl2/f1.bed -b /tmp/tmp1ex4hxl2/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp656faerx/f1.bed -b /tmp/tmp656faerx/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp9qnxw8s2/f1.bed -b /tmp/tmp9qnxw8s2/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpdpt0_w1d/f1.bed -b /tmp/tmpdpt0_w1d/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp19q_vj61/f1.bed -b /tmp/tmp19q_vj61/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmplmxstj7x/f1.bed -b /tmp/tmplmxstj7x/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpx0p7dauz/f1.bed -b /tmp/tmpx0p7dauz/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpq_yti0bc/f1.bed -b /tmp/tmpq_yti0bc/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpylpm5ikv/f1.bed -b /tmp/tmpylpm5ikv/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp0ybljdhi/f1.bed -b /tmp/tmp0ybljdhi/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpxmg9ycon/f1.bed -b /tmp/tmpxmg9ycon/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpx_5u_7j1/f1.bed -b /tmp/tmpx_5u_7j1/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpwov11r8e/f1.bed -b /tmp/tmpwov11r8e/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp86_pxsx7/f1.bed -b /tmp/tmp86_pxsx7/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp1bt7kxx2/f1.bed -b /tmp/tmp1bt7kxx2/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpui0b4slz/f1.bed -b /tmp/tmpui0b4slz/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpw2t3ka62/f1.bed -b /tmp/tmpw2t3ka62/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpiutiwv52/f1.bed -b /tmp/tmpiutiwv52/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp6p7gnh1t/f1.bed -b /tmp/tmp6p7gnh1t/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpxrwjjddy/f1.bed -b /tmp/tmpxrwjjddy/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpk4jfh79c/f1.bed -b /tmp/tmpk4jfh79c/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp30tyzti1/f1.bed -b /tmp/tmp30tyzti1/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpsq4ufwjh/f1.bed -b /tmp/tmpsq4ufwjh/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpc7dhpdwc/f1.bed -b /tmp/tmpc7dhpdwc/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmprl5bav3_/f1.bed -b /tmp/tmprl5bav3_/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpgrgaodib/f1.bed -b /tmp/tmpgrgaodib/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpl9skmfiw/f1.bed -b /tmp/tmpl9skmfiw/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpp2ty3ih0/f1.bed -b /tmp/tmpp2ty3ih0/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpmraxpyle/f1.bed -b /tmp/tmpmraxpyle/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpvxla37g9/f1.bed -b /tmp/tmpvxla37g9/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp63u87gwm/f1.bed -b /tmp/tmp63u87gwm/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmplc3cplcv/f1.bed -b /tmp/tmplc3cplcv/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpei1zbkri/f1.bed -b /tmp/tmpei1zbkri/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmparevdtol/f1.bed -b /tmp/tmparevdtol/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpyz07nnsd/f1.bed -b /tmp/tmpyz07nnsd/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpwh57zuax/f1.bed -b /tmp/tmpwh57zuax/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpla6fayfw/f1.bed -b /tmp/tmpla6fayfw/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpkj4zhc_q/f1.bed -b /tmp/tmpkj4zhc_q/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp_g7qshv8/f1.bed -b /tmp/tmp_g7qshv8/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpdxv7mucw/f1.bed -b /tmp/tmpdxv7mucw/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpuc1dgpek/f1.bed -b /tmp/tmpuc1dgpek/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp9l91r3yw/f1.bed -b /tmp/tmp9l91r3yw/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp7744p8ko/f1.bed -b /tmp/tmp7744p8ko/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpffc8ia61/f1.bed -b /tmp/tmpffc8ia61/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpp4db8q5p/f1.bed -b /tmp/tmpp4db8q5p/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp7tbfoqht/f1.bed -b /tmp/tmp7tbfoqht/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp5vhfbda2/f1.bed -b /tmp/tmp5vhfbda2/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpqi0w88mt/f1.bed -b /tmp/tmpqi0w88mt/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpi_fpu5qj/f1.bed -b /tmp/tmpi_fpu5qj/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp2cey_ffo/f1.bed -b /tmp/tmp2cey_ffo/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpb_h329s_/f1.bed -b /tmp/tmpb_h329s_/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpw_wd1_zk/f1.bed -b /tmp/tmpw_wd1_zk/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpixn17pc0/f1.bed -b /tmp/tmpixn17pc0/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp2xd1ej57/f1.bed -b /tmp/tmp2xd1ej57/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp8ttdxo1f/f1.bed -b /tmp/tmp8ttdxo1f/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp1v44ne9j/f1.bed -b /tmp/tmp1v44ne9j/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpo7dsumdt/f1.bed -b /tmp/tmpo7dsumdt/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpjod1ifx9/f1.bed -b /tmp/tmpjod1ifx9/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp_0q7k9b0/f1.bed -b /tmp/tmp_0q7k9b0/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpgs0ou2ns/f1.bed -b /tmp/tmpgs0ou2ns/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpa4fx78cm/f1.bed -b /tmp/tmpa4fx78cm/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpa13rqpcx/f1.bed -b /tmp/tmpa13rqpcx/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp9ygxg67f/f1.bed -b /tmp/tmp9ygxg67f/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpehlf4wvi/f1.bed -b /tmp/tmpehlf4wvi/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp4z8ttxsr/f1.bed -b /tmp/tmp4z8ttxsr/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpagt50z0v/f1.bed -b /tmp/tmpagt50z0v/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpwzxalk2b/f1.bed -b /tmp/tmpwzxalk2b/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp3grp2_yg/f1.bed -b /tmp/tmp3grp2_yg/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmppe0paw11/f1.bed -b /tmp/tmppe0paw11/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp6wvnvpsy/f1.bed -b /tmp/tmp6wvnvpsy/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp6qjn06dd/f1.bed -b /tmp/tmp6qjn06dd/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpbv4azi05/f1.bed -b /tmp/tmpbv4azi05/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmptsbn3tsi/f1.bed -b /tmp/tmptsbn3tsi/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp81nhrolk/f1.bed -b /tmp/tmp81nhrolk/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpocef1rl8/f1.bed -b /tmp/tmpocef1rl8/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpajdzdi3f/f1.bed -b /tmp/tmpajdzdi3f/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpscxgqyqc/f1.bed -b /tmp/tmpscxgqyqc/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmphfaohxb2/f1.bed -b /tmp/tmphfaohxb2/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp9wuyuphb/f1.bed -b /tmp/tmp9wuyuphb/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpemapzdzs/f1.bed -b /tmp/tmpemapzdzs/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpl6otafoc/f1.bed -b /tmp/tmpl6otafoc/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpt118ygzq/f1.bed -b /tmp/tmpt118ygzq/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpc8c1u25c/f1.bed -b /tmp/tmpc8c1u25c/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpm89k7hxc/f1.bed -b /tmp/tmpm89k7hxc/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpgegs2cjw/f1.bed -b /tmp/tmpgegs2cjw/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpxt2lj3a4/f1.bed -b /tmp/tmpxt2lj3a4/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp9tg1wngh/f1.bed -b /tmp/tmp9tg1wngh/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpf55u7y6t/f1.bed -b /tmp/tmpf55u7y6t/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpocnxeuy8/f1.bed -b /tmp/tmpocnxeuy8/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpso_hs10j/f1.bed -b /tmp/tmpso_hs10j/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpbe_50h5s/f1.bed -b /tmp/tmpbe_50h5s/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp_6bcy8od/f1.bed -b /tmp/tmp_6bcy8od/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpxafocpub/f1.bed -b /tmp/tmpxafocpub/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpnmlsdwbx/f1.bed -b /tmp/tmpnmlsdwbx/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpugixf_dm/f1.bed -b /tmp/tmpugixf_dm/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpc51sfuon/f1.bed -b /tmp/tmpc51sfuon/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp3k5xp0by/f1.bed -b /tmp/tmp3k5xp0by/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp3ri8cqxl/f1.bed -b /tmp/tmp3ri8cqxl/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpkg3qlg9q/f1.bed -b /tmp/tmpkg3qlg9q/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpy6130wkv/f1.bed -b /tmp/tmpy6130wkv/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpedy_9qr2/f1.bed -b /tmp/tmpedy_9qr2/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmptt44ytb4/f1.bed -b /tmp/tmptt44ytb4/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpoa16vaoj/f1.bed -b /tmp/tmpoa16vaoj/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpengglexe/f1.bed -b /tmp/tmpengglexe/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp_a606wma/f1.bed -b /tmp/tmp_a606wma/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpu8504qjs/f1.bed -b /tmp/tmpu8504qjs/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpzachcppe/f1.bed -b /tmp/tmpzachcppe/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp414xonb8/f1.bed -b /tmp/tmp414xonb8/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpmpoch5vm/f1.bed -b /tmp/tmpmpoch5vm/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpej74ywyh/f1.bed -b /tmp/tmpej74ywyh/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp36b7itft/f1.bed -b /tmp/tmp36b7itft/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpp8my9w2n/f1.bed -b /tmp/tmpp8my9w2n/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpso90aa_b/f1.bed -b /tmp/tmpso90aa_b/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp10osa08t/f1.bed -b /tmp/tmp10osa08t/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpx_t50tw1/f1.bed -b /tmp/tmpx_t50tw1/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpdoyocr12/f1.bed -b /tmp/tmpdoyocr12/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmplsyjedm4/f1.bed -b /tmp/tmplsyjedm4/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp6siwc50k/f1.bed -b /tmp/tmp6siwc50k/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpu94ee5m0/f1.bed -b /tmp/tmpu94ee5m0/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpwoa8c03c/f1.bed -b /tmp/tmpwoa8c03c/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp28sorqk9/f1.bed -b /tmp/tmp28sorqk9/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpe28hxyv3/f1.bed -b /tmp/tmpe28hxyv3/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmph827otel/f1.bed -b /tmp/tmph827otel/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpkh1ydfck/f1.bed -b /tmp/tmpkh1ydfck/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmphejbftul/f1.bed -b /tmp/tmphejbftul/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpnscjcsvy/f1.bed -b /tmp/tmpnscjcsvy/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp2nfc1u4x/f1.bed -b /tmp/tmp2nfc1u4x/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp3v_2ekvf/f1.bed -b /tmp/tmp3v_2ekvf/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpffzsla6t/f1.bed -b /tmp/tmpffzsla6t/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpp_kuxo_q/f1.bed -b /tmp/tmpp_kuxo_q/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpookaf5p5/f1.bed -b /tmp/tmpookaf5p5/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpipj84t6a/f1.bed -b /tmp/tmpipj84t6a/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpksz6ux1l/f1.bed -b /tmp/tmpksz6ux1l/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpnkciu_mw/f1.bed -b /tmp/tmpnkciu_mw/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp3vte1q87/f1.bed -b /tmp/tmp3vte1q87/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmprjfb0vj3/f1.bed -b /tmp/tmprjfb0vj3/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp9zr17xs4/f1.bed -b /tmp/tmp9zr17xs4/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpdf4js3hh/f1.bed -b /tmp/tmpdf4js3hh/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp64ejdpar/f1.bed -b /tmp/tmp64ejdpar/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmplt04gaey/f1.bed -b /tmp/tmplt04gaey/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp_n95hlw_/f1.bed -b /tmp/tmp_n95hlw_/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp7ad9hysx/f1.bed -b /tmp/tmp7ad9hysx/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpdr1tgfpx/f1.bed -b /tmp/tmpdr1tgfpx/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpzarc9yjv/f1.bed -b /tmp/tmpzarc9yjv/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpuoem2hlq/f1.bed -b /tmp/tmpuoem2hlq/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpz3w2kv7n/f1.bed -b /tmp/tmpz3w2kv7n/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp275ojc_n/f1.bed -b /tmp/tmp275ojc_n/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpuae5fhw7/f1.bed -b /tmp/tmpuae5fhw7/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpeaj3p033/f1.bed -b /tmp/tmpeaj3p033/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpp9ngo1lz/f1.bed -b /tmp/tmpp9ngo1lz/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpvvyftq66/f1.bed -b /tmp/tmpvvyftq66/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp3zimoj9y/f1.bed -b /tmp/tmp3zimoj9y/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpddarvp9v/f1.bed -b /tmp/tmpddarvp9v/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp5yfc9gjb/f1.bed -b /tmp/tmp5yfc9gjb/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpn433qye0/f1.bed -b /tmp/tmpn433qye0/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp55vjb9wc/f1.bed -b /tmp/tmp55vjb9wc/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpo9ffblp_/f1.bed -b /tmp/tmpo9ffblp_/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpgw9l59ux/f1.bed -b /tmp/tmpgw9l59ux/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpgzy9i70i/f1.bed -b /tmp/tmpgzy9i70i/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmplrnd4ou_/f1.bed -b /tmp/tmplrnd4ou_/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpdjx65f44/f1.bed -b /tmp/tmpdjx65f44/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp1zv8wv69/f1.bed -b /tmp/tmp1zv8wv69/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpf4zevu52/f1.bed -b /tmp/tmpf4zevu52/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp20db9wvu/f1.bed -b /tmp/tmp20db9wvu/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpwim4wmf0/f1.bed -b /tmp/tmpwim4wmf0/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp85k93_pi/f1.bed -b /tmp/tmp85k93_pi/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpdvoquh93/f1.bed -b /tmp/tmpdvoquh93/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ____________ test_three_in_a_row[strandedness_chain6-method_chain6] ____________ [gw5] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', False), method_chain = ('set_union', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('set_union', 'join'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E (and 184 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2B0yDvzLY3RhoGRAQsAAFGMAxY=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ___________ test_three_in_a_row[strandedness_chain78-method_chain78] ___________ [gw4] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', 'same') method_chain = ('intersect', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('intersect', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:145 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 E (and 27 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BAAEYUCgwAAD4AAw==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ___________ test_three_in_a_row[strandedness_chain14-method_chain14] ___________ [gw7] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', False), method_chain = ('overlap', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('overlap', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:33 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:41 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:17 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:21 E (and 142 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ___________ test_three_in_a_row[strandedness_chain63-method_chain63] ___________ [gw9] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', 'same'), method_chain = ('overlap', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('overlap', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E (and 154 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BAAEYUCgwAAD4AAw==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ___________ test_three_in_a_row[strandedness_chain38-method_chain38] ___________ [gw8] linux -- Python 3.12.6 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 880, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1722, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 292, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', False), | method_chain=('subtract', 'nearest'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 4 | 5 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=Empty PyRanges, | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 33 | 34 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:73 | (and 27 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2RkAAJGIAQhZiiNEIHwoJQCjAMAA4oAMg==') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 4384, in subtract | other_clusters = other.merge(strand=strand) | ^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 347, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', False), | method_chain=('subtract', 'nearest'), | gr=Empty PyRanges, | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=Empty PyRanges, # or any other generated value | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:143 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:30 | (and 19 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2CAA0YUCgIAAEAAAw==') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 10 | a | 0 | ... | | chr1 | 5 | 7 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 5 | 1532 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 5 | 1532 | a | 0 | ... | | chr1 | 65537 | 66017 | a | 0 | ... | | chr1 | 5 | 3564 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 9 rows and 12 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 258 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________________ test_k_nearest[downstream-False-same-last] __________________ [gw3] linux -- Python 3.12.6 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 880, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 510, in test_k_nearest | @pytest.mark.explore | ^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1722, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 548, in test_k_nearest | result = gr.k_nearest( | ^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2450, in k_nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 180, in _nearest | df = __nearest(d1, d2, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 115, in nearest_previous | lidx, ridx, dist = nearest_previous_idx(d1, d2, d1.__k__.values, ties) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 28, in nearest_previous_idx | lidx, ridx_pos, dist = k_nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/k_nearest.pyx", line 28, in sorted_nearest.src.k_nearest.k_nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_k_nearest( | nearest_how='downstream', | overlap=False, | strandedness='same', | ties='last', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr2 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr2 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:14 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:15 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:160 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:171 | (and 40 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2SAAEYGOGBkxCIGAACmAAc=') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 548, in test_k_nearest | result = gr.k_nearest( | ^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2450, in k_nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 180, in _nearest | df = __nearest(d1, d2, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 140, in nearest_next | lidx, ridx, dist = nearest_next_idx(d1, d2, d1.__k__.values, ties) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 56, in nearest_next_idx | lidx, ridx_pos, dist = k_nearest_next_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/k_nearest.pyx", line 55, in sorted_nearest.src.k_nearest.k_nearest_next_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_k_nearest( | nearest_how='downstream', | overlap=False, | strandedness='same', | ties='last', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:160 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:171 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:41 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:42 | (and 41 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2TABIxYxAAAZAAD') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmphons_v8j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphons_v8j/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpy9i30nn5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy9i30nn5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpk6pqs9ri/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk6pqs9ri/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9deej1vc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9deej1vc/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8t_ft6ua/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8t_ft6ua/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmprrftcba3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprrftcba3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyke49k5e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyke49k5e/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpymt_na22/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpymt_na22/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9o17v0m4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9o17v0m4/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuopd57ki/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuopd57ki/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpabz8ilwv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpabz8ilwv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjkbjb_6_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjkbjb_6_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpv9f62r3n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv9f62r3n/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmppy68d9ms/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppy68d9ms/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8m8tmg5d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8m8tmg5d/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3i6z9ixp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3i6z9ixp/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmprwzns_xl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprwzns_xl/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpr4r_w1o5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr4r_w1o5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp37_fqkj4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp37_fqkj4/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpaowjirmu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaowjirmu/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0ntktqwc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0ntktqwc/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjc2vr6yc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjc2vr6yc/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp39e_a62l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp39e_a62l/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6xadmekp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6xadmekp/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwvgf6k9m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwvgf6k9m/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmphbfaff_9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphbfaff_9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmphopuu5iy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphopuu5iy/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpthw9eze2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpthw9eze2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpztf5sht6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpztf5sht6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpp43om2d0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp43om2d0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1yfudrv9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1yfudrv9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpx84li3pv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx84li3pv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpe9o5o991/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe9o5o991/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbci02ra6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbci02ra6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5ubxf94d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5ubxf94d/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4ynjqqv3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4ynjqqv3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmplrp8x7ky/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplrp8x7ky/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp75l86gfn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp75l86gfn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzppessd2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzppessd2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwtvnx2pc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwtvnx2pc/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpp5t4uyv4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp5t4uyv4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpy8r0fm60/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy8r0fm60/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp614r1_zq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp614r1_zq/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4bxj52kd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4bxj52kd/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkx3k1ic2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkx3k1ic2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpl9fd9ebn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl9fd9ebn/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmph0cu__1p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph0cu__1p/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9r4104l9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9r4104l9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwvane7l1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwvane7l1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0ljw85bm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0ljw85bm/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpone9fyk3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpone9fyk3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpz9udgpd7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz9udgpd7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5dq7fa8g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5dq7fa8g/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdea2js0e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdea2js0e/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpflqb6jmr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpflqb6jmr/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmphjemx29r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphjemx29r/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_nm00xtv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_nm00xtv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9goqr_60/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9goqr_60/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyl_s6rac/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyl_s6rac/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6uiln5ke/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6uiln5ke/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpco0l4d3u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpco0l4d3u/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmplnfwnvri/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplnfwnvri/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6_56_iqc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6_56_iqc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7qwxdvvz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7qwxdvvz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_2dqxkvr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_2dqxkvr/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6glfl0vv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6glfl0vv/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp28tj_xqj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp28tj_xqj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9x825xf6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9x825xf6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvq80uxhj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvq80uxhj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_0vrjc5q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_0vrjc5q/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4us_e1pa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4us_e1pa/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4pnrf0sd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4pnrf0sd/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgogdcogc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgogdcogc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6ls5mqph/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6ls5mqph/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpi6rcsb0p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi6rcsb0p/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpc6la_1ib/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc6la_1ib/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpv3vmm1i1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv3vmm1i1/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpaw1ztk2v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaw1ztk2v/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7sjpn9ny/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7sjpn9ny/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmk55h5g8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmk55h5g8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp00qzjgpd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp00qzjgpd/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsd2pwxqh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsd2pwxqh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpa0_c87lt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa0_c87lt/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp80juhxcd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp80juhxcd/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpryw5e10d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpryw5e10d/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmprgg63hk9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprgg63hk9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyw0ivcpv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyw0ivcpv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmprz9ux3c9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprz9ux3c9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdfpol7tt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdfpol7tt/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpji07bz9w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpji07bz9w/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3sdjh7rg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3sdjh7rg/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpz51w5q7a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz51w5q7a/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjd7ee3w_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjd7ee3w_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3idmo6cm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3idmo6cm/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmptu83_42k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptu83_42k/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmppo9kj4m2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppo9kj4m2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7u_ya28f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7u_ya28f/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmplmq_30__/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplmq_30__/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxdr1mfd0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxdr1mfd0/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp79zb7c7w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp79zb7c7w/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2adqizau/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2adqizau/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp70zinlpe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp70zinlpe/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpj3fj6ei9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj3fj6ei9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmppe653n7p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppe653n7p/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmphcovf82i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphcovf82i/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyk7n27pk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyk7n27pk/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpiv3qz_0u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiv3qz_0u/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpacvqdvwg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpacvqdvwg/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpx9a03zhl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx9a03zhl/f2.bed) ----------------------------- Captured stderr call ----------------------------- Warning: Fewer hits (1) found on chrM than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrM than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. ___________ test_three_in_a_row[strandedness_chain52-method_chain52] ___________ [gw10] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', 'same'), method_chain = ('set_union', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('set_union', 'nearest'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E (and 183 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2CAA0YGLAAAADUAAg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ________________________ test_nearest[None-True-False] _________________________ [gw1] linux -- Python 3.12.6 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 880, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 323, in test_nearest | @pytest.mark.parametrize("nearest_how,overlap,strandedness", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1722, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 351, in test_nearest | result = gr.nearest( | ^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 292, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_nearest( | nearest_how=None, | overlap=True, | strandedness=False, | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:11 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:12 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:101 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 | (and 65 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2TABIxQkhGJxwAAAIoABg==') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 359, in test_nearest | compare_results_nearest(bedtools_df, result) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 107, in compare_results_nearest | assert_df_equal(result_df, bedtools_df) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/helpers.py", line 60, in assert_df_equal | pd.testing.assert_frame_equal(df1, df2) | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 1279, in assert_frame_equal | assert_series_equal( | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 975, in assert_series_equal | assert_attr_equal("dtype", left, right, obj=f"Attributes of {obj}") | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 421, in assert_attr_equal | raise_assert_detail(obj, msg, left_attr, right_attr) | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 614, in raise_assert_detail | raise AssertionError(msg) | AssertionError: Attributes of DataFrame.iloc[:, 4] (column name="Distance") are different | | Attribute "dtype" are different | [left]: int32 | [right]: int64 | Falsifying example: test_nearest( | nearest_how=None, | overlap=True, | strandedness=False, | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/init.py:174 | (and 453 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2TABIwoFBgAAABtAAQ=') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpl6aa33_3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl6aa33_3/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzzntvqv1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzzntvqv1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmph9h286rc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph9h286rc/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 258 - 0 1 chr1 9 15 + 0 2 chr1 9 266 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 9 | 15 | a | 0 | ... | | chr1 | 1 | 258 | a | 0 | ... | | chr1 | 9 | 266 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 1 258 - 0 0 chr1 9 15 + 0 2 chr1 9 266 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 258 - 0 1 chr1 9 15 + 0 2 chr1 9 266 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 258 - 0 1 chr1 9 15 + 0 2 chr1 9 266 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 258 - 0 1 chr1 9 15 + 0 2 chr1 9 266 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpudlbqz0f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpudlbqz0f/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 258 - 0 1 chr1 9 15 + 0 2 chr1 9 266 - 0 3 chr16 9 14 - 0 4 chr2 9 266 - 0 5 chr2 9 266 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 9 | 15 | a | 0 | ... | | chr1 | 1 | 258 | a | 0 | ... | | chr1 | 9 | 266 | a | 0 | ... | | chr2 | 9 | 266 | a | 0 | ... | | chr2 | 9 | 266 | a | 0 | ... | | chr16 | 9 | 14 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 1 258 - 0 5 chr16 9 14 - 0 0 chr1 9 15 + 0 2 chr1 9 266 - 0 3 chr2 9 266 - 0 4 chr2 9 266 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 258 - 0 3 chr16 9 14 - 0 1 chr1 9 15 + 0 2 chr1 9 266 - 0 4 chr2 9 266 - 0 5 chr2 9 266 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 258 - 0 1 chr1 9 15 + 0 2 chr1 9 266 - 0 3 chr16 9 14 - 0 4 chr2 9 266 - 0 5 chr2 9 266 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 258 - 0 1 chr1 9 15 + 0 2 chr1 9 266 - 0 3 chr16 9 14 - 0 4 chr2 9 266 - 0 5 chr2 9 266 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpu0v9woj8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu0v9woj8/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 258 - 0 1 chr1 9 15 + 0 2 chr1 9 266 - 0 4 chr2 9 266 - 0 5 chr2 9 266 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 9 | 15 | a | 0 | ... | | chr1 | 1 | 258 | a | 0 | ... | | chr1 | 9 | 266 | a | 0 | ... | | chr2 | 9 | 266 | a | 0 | ... | | chr2 | 9 | 266 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 1 258 - 0 0 chr1 9 15 + 0 2 chr1 9 266 - 0 3 chr2 9 266 - 0 4 chr2 9 266 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 258 - 0 1 chr1 9 15 + 0 2 chr1 9 266 - 0 4 chr2 9 266 - 0 5 chr2 9 266 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 258 - 0 1 chr1 9 15 + 0 2 chr1 9 266 - 0 3 chr2 9 266 - 0 4 chr2 9 266 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 258 - 0 1 chr1 9 15 + 0 2 chr1 9 266 - 0 3 chr2 9 266 - 0 4 chr2 9 266 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp13ncojr3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp13ncojr3/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 6 12 + 0 1 chr1 257 514 - 0 2 chr1 257 514 - 0 4 chr2 257 514 - 0 5 chr2 257 514 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 6 | 12 | a | 0 | ... | | chr1 | 257 | 514 | a | 0 | ... | | chr1 | 257 | 514 | a | 0 | ... | | chr2 | 257 | 514 | a | 0 | ... | | chr2 | 257 | 514 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 6 12 + 0 1 chr1 257 514 - 0 2 chr1 257 514 - 0 3 chr2 257 514 - 0 4 chr2 257 514 - 0 df2 Chromosome Start End Strand Distance 0 chr1 6 12 + 0 1 chr1 257 514 - 0 2 chr1 257 514 - 0 4 chr2 257 514 - 0 5 chr2 257 514 - 0 Actual Chromosome Start End Strand Distance 0 chr1 6 12 + 0 1 chr1 257 514 - 0 2 chr1 257 514 - 0 3 chr2 257 514 - 0 4 chr2 257 514 - 0 Expected Chromosome Start End Strand Distance 0 chr1 6 12 + 0 1 chr1 257 514 - 0 2 chr1 257 514 - 0 3 chr2 257 514 - 0 4 chr2 257 514 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjanozrxr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjanozrxr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjv2klf82/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjv2klf82/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 6 12 + 0 1 chr1 257 514 - 0 2 chr1 257 514 - 0 3 chr16 5 10 - 0 4 chr2 257 514 - 0 5 chr2 257 514 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 6 | 12 | a | 0 | ... | | chr1 | 257 | 514 | a | 0 | ... | | chr1 | 257 | 514 | a | 0 | ... | | chr2 | 257 | 514 | a | 0 | ... | | chr2 | 257 | 514 | a | 0 | ... | | chr16 | 5 | 10 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 5 chr16 5 10 - 0 0 chr1 6 12 + 0 1 chr1 257 514 - 0 2 chr1 257 514 - 0 3 chr2 257 514 - 0 4 chr2 257 514 - 0 df2 Chromosome Start End Strand Distance 3 chr16 5 10 - 0 0 chr1 6 12 + 0 1 chr1 257 514 - 0 2 chr1 257 514 - 0 4 chr2 257 514 - 0 5 chr2 257 514 - 0 Actual Chromosome Start End Strand Distance 0 chr1 6 12 + 0 1 chr1 257 514 - 0 2 chr1 257 514 - 0 3 chr16 5 10 - 0 4 chr2 257 514 - 0 5 chr2 257 514 - 0 Expected Chromosome Start End Strand Distance 0 chr1 6 12 + 0 1 chr1 257 514 - 0 2 chr1 257 514 - 0 3 chr16 5 10 - 0 4 chr2 257 514 - 0 5 chr2 257 514 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp952lblm0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp952lblm0/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsz5ph2rl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsz5ph2rl/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpju5_n8a8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpju5_n8a8/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuz2ilyf1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuz2ilyf1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphnwn418t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphnwn418t/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3yuxixws/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3yuxixws/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpi2u6cvbx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi2u6cvbx/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpco0jxoc_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpco0jxoc_/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbpb2co8q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbpb2co8q/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbhx35nlk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbhx35nlk/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6yno729j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6yno729j/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmfa9ohdy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmfa9ohdy/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzo9cs7_1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzo9cs7_1/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp008hcyr1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp008hcyr1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpg5zs3sge/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg5zs3sge/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmph9oloooz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph9oloooz/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpa6tajbni/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa6tajbni/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp971azzv8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp971azzv8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdycrqfkw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdycrqfkw/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpviojd0sr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpviojd0sr/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2sk6oelw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2sk6oelw/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1l1rngz3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1l1rngz3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpv6kxs8fo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv6kxs8fo/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpik7g6ndy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpik7g6ndy/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5sv81nel/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5sv81nel/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpz742amcn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz742amcn/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpigfdyang/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpigfdyang/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwov1qmbd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwov1qmbd/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp54bqvsof/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp54bqvsof/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqyz8p2gs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqyz8p2gs/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpje3ge0kq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpje3ge0kq/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpthmvq2wn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpthmvq2wn/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbdswb4h7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbdswb4h7/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkfw3dbvf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkfw3dbvf/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpub4ezhfu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpub4ezhfu/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqga00clt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqga00clt/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpimu0mbj1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpimu0mbj1/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpujd6r1t1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpujd6r1t1/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4fbbwy9a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4fbbwy9a/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzze89czs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzze89czs/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxup7d0qu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxup7d0qu/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxq4c8ljc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxq4c8ljc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpk_t4_xyo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk_t4_xyo/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp40u1s3qh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp40u1s3qh/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcyzgqjpi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcyzgqjpi/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfc3ef8hi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfc3ef8hi/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvpxmtyyd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvpxmtyyd/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0xd2r7dn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0xd2r7dn/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpr9qp1a1s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr9qp1a1s/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfk7754oc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfk7754oc/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5t_c24un/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5t_c24un/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjt4ir_ry/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjt4ir_ry/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp75_x_py0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp75_x_py0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsexz1420/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsexz1420/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_cnfqsnc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_cnfqsnc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppdpy2n4h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppdpy2n4h/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprxsfi3a1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprxsfi3a1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpq0f4efvc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq0f4efvc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp25c8lrox/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp25c8lrox/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjhs9kape/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjhs9kape/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpafhhy5ak/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpafhhy5ak/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvp7jhc7i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvp7jhc7i/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjx7wytws/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjx7wytws/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbq_pft4x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbq_pft4x/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxta34c9d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxta34c9d/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpogsf65dz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpogsf65dz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3l2z907n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3l2z907n/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprd5fq81h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprd5fq81h/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpi7rpbaz3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi7rpbaz3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7cazakf5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7cazakf5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2u1vpe4q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2u1vpe4q/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8oadqzp3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8oadqzp3/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpc8_5syet/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc8_5syet/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpz44kdpym/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz44kdpym/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnrgo8i94/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnrgo8i94/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp61dyro6j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp61dyro6j/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpimy2tl3d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpimy2tl3d/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbq_t5hpd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbq_t5hpd/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwtu5kjtv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwtu5kjtv/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgx6ykn84/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgx6ykn84/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7w_f6yic/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7w_f6yic/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5mmanr33/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5mmanr33/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqw555790/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqw555790/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpeaaz2r5e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpeaaz2r5e/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0sqx4asj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0sqx4asj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnlvuojw1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnlvuojw1/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdd_nmf49/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdd_nmf49/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0p3o4j1t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0p3o4j1t/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpf1hf72od/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf1hf72od/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxcs8jbd6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxcs8jbd6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3ewoazmx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3ewoazmx/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpw0qpx6ye/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw0qpx6ye/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ____________________ test_nearest[downstream-True-opposite] ____________________ [gw2] linux -- Python 3.12.6 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 880, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 323, in test_nearest | @pytest.mark.parametrize("nearest_how,overlap,strandedness", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1722, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 3 distinct failures. (3 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 351, in test_nearest | result = gr.nearest( | ^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 115, in _nearest | r_idx, dist = _next_nonoverlapping(df_to_find_nearest_in.End, | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 62, in _next_nonoverlapping | r_idx, dist = nearest_next_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 34, in sorted_nearest.src.sorted_nearest.nearest_next_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_nearest( | nearest_how='downstream', | overlap=True, | strandedness='opposite', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | (and 124 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2QAA0Y4gU6BmQAApQAH') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 351, in test_nearest | result = gr.nearest( | ^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 118, in _nearest | r_idx, dist = _previous_nonoverlapping(df_to_find_nearest_in.Start, | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_nearest( | nearest_how='downstream', | overlap=True, | strandedness='opposite', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | (and 127 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2QAA0YGOGBkRBKCsgEApQAH') as a decorator on your test case +---------------- 3 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 359, in test_nearest | compare_results_nearest(bedtools_df, result) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 107, in compare_results_nearest | assert_df_equal(result_df, bedtools_df) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/helpers.py", line 60, in assert_df_equal | pd.testing.assert_frame_equal(df1, df2) | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 1279, in assert_frame_equal | assert_series_equal( | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 975, in assert_series_equal | assert_attr_equal("dtype", left, right, obj=f"Attributes of {obj}") | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 421, in assert_attr_equal | raise_assert_detail(obj, msg, left_attr, right_attr) | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 614, in raise_assert_detail | raise AssertionError(msg) | AssertionError: Attributes of DataFrame.iloc[:, 4] (column name="Distance") are different | | Attribute "dtype" are different | [left]: int32 | [right]: int64 | Falsifying example: test_nearest( | nearest_how='downstream', | overlap=True, | strandedness='opposite', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | (and 460 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2QAA0YGBGDEEGIEAACLAAY=') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpx2deh2op/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx2deh2op/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpios0pdkv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpios0pdkv/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpka48d7q7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpka48d7q7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4byyjszq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4byyjszq/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp59asgev8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp59asgev8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3rsbvvv3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3rsbvvv3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpto4e87h_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpto4e87h_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpd47zlrb9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd47zlrb9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4me4urzi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4me4urzi/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 258 - 0 1 chr1 3 6 - 0 2 chr1 3 6 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 1 | 258 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 1 258 - 0 0 chr1 3 6 - 0 2 chr1 3 6 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 258 - 0 1 chr1 3 6 - 0 2 chr1 3 6 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 258 - 0 1 chr1 3 6 - 0 2 chr1 3 6 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 258 - 0 1 chr1 3 6 - 0 2 chr1 3 6 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphxozyzw7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphxozyzw7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpldgqaf3i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpldgqaf3i/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_runotr0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_runotr0/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjilh_reh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjilh_reh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0kcsstw_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0kcsstw_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpf37lc7_0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf37lc7_0/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 65537 65538 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 65538 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 65537 65538 - 0 df2 Chromosome Start End Strand Distance 0 chr1 65537 65538 - 0 Actual Chromosome Start End Strand Distance 0 chr1 65537 65538 - 0 Expected Chromosome Start End Strand Distance 0 chr1 65537 65538 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpu44y1g13/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu44y1g13/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsi17c49b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsi17c49b/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprcql6bcz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprcql6bcz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8nm3vrve/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8nm3vrve/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0c1pkv2u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0c1pkv2u/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 65537 65538 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 65538 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 65537 65538 - 0 df2 Chromosome Start End Strand Distance 0 chr1 65537 65538 - 0 Actual Chromosome Start End Strand Distance 0 chr1 65537 65538 - 0 Expected Chromosome Start End Strand Distance 0 chr1 65537 65538 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpinz367ck/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpinz367ck/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4s4gqg65/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4s4gqg65/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptun73yuk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptun73yuk/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 65537 65538 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 65538 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 65537 65538 - 0 df2 Chromosome Start End Strand Distance 0 chr1 65537 65538 - 0 Actual Chromosome Start End Strand Distance 0 chr1 65537 65538 - 0 Expected Chromosome Start End Strand Distance 0 chr1 65537 65538 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpl0y4r_0a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl0y4r_0a/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 65537 65538 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 65538 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 65537 65538 - 0 df2 Chromosome Start End Strand Distance 0 chr1 65537 65538 - 0 Actual Chromosome Start End Strand Distance 0 chr1 65537 65538 - 0 Expected Chromosome Start End Strand Distance 0 chr1 65537 65538 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpk559tldv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk559tldv/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxx6ld7op/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxx6ld7op/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9nkna111/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9nkna111/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp92z0d6vb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp92z0d6vb/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpymti30je/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpymti30je/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_evof5ca/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_evof5ca/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxfq2iq6p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxfq2iq6p/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 65537 65538 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 65538 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 65537 65538 + 0 df2 Chromosome Start End Strand Distance 0 chr1 65537 65538 + 0 Actual Chromosome Start End Strand Distance 0 chr1 65537 65538 + 0 Expected Chromosome Start End Strand Distance 0 chr1 65537 65538 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpja99kz9v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpja99kz9v/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9i9_5n0s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9i9_5n0s/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3lla4905/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3lla4905/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyblhrc5q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyblhrc5q/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 258 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 258 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 258 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 258 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 258 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 258 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpj6mwef6o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj6mwef6o/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmyc_kn6t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmyc_kn6t/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2zj2e0si/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2zj2e0si/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 257 258 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 257 | 258 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 257 258 + 0 df2 Chromosome Start End Strand Distance 0 chr1 257 258 + 0 Actual Chromosome Start End Strand Distance 0 chr1 257 258 + 0 Expected Chromosome Start End Strand Distance 0 chr1 257 258 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwnw18tpf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwnw18tpf/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 257 258 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 257 | 258 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 257 258 + 0 df2 Chromosome Start End Strand Distance 0 chr1 257 258 + 0 Actual Chromosome Start End Strand Distance 0 chr1 257 258 + 0 Expected Chromosome Start End Strand Distance 0 chr1 257 258 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp297b_ijm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp297b_ijm/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 257 258 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 257 | 258 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 257 258 + 0 df2 Chromosome Start End Strand Distance 0 chr1 257 258 + 0 Actual Chromosome Start End Strand Distance 0 chr1 257 258 + 0 Expected Chromosome Start End Strand Distance 0 chr1 257 258 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdzs9mwuh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdzs9mwuh/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 257 258 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 257 | 258 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 257 258 + 0 df2 Chromosome Start End Strand Distance 0 chr1 257 258 + 0 Actual Chromosome Start End Strand Distance 0 chr1 257 258 + 0 Expected Chromosome Start End Strand Distance 0 chr1 257 258 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1wwu4_yr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1wwu4_yr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprgb8y0iw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprgb8y0iw/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 257 258 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 257 | 258 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 257 258 + 0 df2 Chromosome Start End Strand Distance 0 chr1 257 258 + 0 Actual Chromosome Start End Strand Distance 0 chr1 257 258 + 0 Expected Chromosome Start End Strand Distance 0 chr1 257 258 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9yxnq0t5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9yxnq0t5/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 257 258 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 257 | 258 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 257 258 + 0 df2 Chromosome Start End Strand Distance 0 chr1 257 258 + 0 Actual Chromosome Start End Strand Distance 0 chr1 257 258 + 0 Expected Chromosome Start End Strand Distance 0 chr1 257 258 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcq3xgr8k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcq3xgr8k/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 257 258 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 257 | 258 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 257 258 + 0 df2 Chromosome Start End Strand Distance 0 chr1 257 258 + 0 Actual Chromosome Start End Strand Distance 0 chr1 257 258 + 0 Expected Chromosome Start End Strand Distance 0 chr1 257 258 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpagw7tlsi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpagw7tlsi/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 258 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 258 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 258 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 258 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 258 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 258 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmph5fzc6a2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph5fzc6a2/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 258 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 258 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 258 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 258 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 258 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 258 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpp9yxrer2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp9yxrer2/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 258 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 258 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 258 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 258 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 258 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 258 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphpj6_051/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphpj6_051/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 258 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 258 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 258 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 258 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 258 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 258 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp537fhxv7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp537fhxv7/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpq7gaja66/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq7gaja66/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbhnkbao6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbhnkbao6/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdl8wpm2i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdl8wpm2i/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqwn3twzc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqwn3twzc/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7vxw5vfh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7vxw5vfh/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp851qdqsr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp851qdqsr/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyfmqwjbl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyfmqwjbl/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0acvbpk0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0acvbpk0/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0ux5vlak/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0ux5vlak/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpiei77sm8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiei77sm8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpepgy9lsl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpepgy9lsl/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvntpa4y7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvntpa4y7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpci5xbfo7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpci5xbfo7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphj248l5o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphj248l5o/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 258 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 258 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 258 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 258 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 258 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 258 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkyoi323z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkyoi323z/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpoy0nhag0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoy0nhag0/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8h5ji8tk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8h5ji8tk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphygpmnt_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphygpmnt_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp72m9j8g1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp72m9j8g1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpt9ugnzcp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt9ugnzcp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcjaaeh3v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcjaaeh3v/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpv0c0lu2s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv0c0lu2s/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpq_8spgv0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq_8spgv0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnexro7cw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnexro7cw/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpw_3nli1c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw_3nli1c/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdf7vqlra/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdf7vqlra/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5earqi8h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5earqi8h/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptjp4nf40/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptjp4nf40/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjq3iw_b7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjq3iw_b7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpa_6d58kc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa_6d58kc/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 3 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 3 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 3 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 3 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 3 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4rppgtev/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4rppgtev/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp27qoxg9m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp27qoxg9m/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpienetxiy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpienetxiy/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkmothr1x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkmothr1x/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1g6c_19a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1g6c_19a/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmperh_2i7c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmperh_2i7c/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjpxqbvco/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjpxqbvco/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpiss0aft7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiss0aft7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmps8aqb8ys/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps8aqb8ys/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2j3ymxdl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2j3ymxdl/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpc832sps5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc832sps5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpf4gmibbd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf4gmibbd/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpeexrt4h1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpeexrt4h1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3wxv7uss/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3wxv7uss/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxq3g1f7i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxq3g1f7i/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ___________ test_three_in_a_row[strandedness_chain25-method_chain25] ___________ [gw6] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', False), method_chain = ('nearest', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('nearest', 'intersect'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:53 E (and 28 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2RAAowQkhGZh85kAAAA6QAH') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain68-method_chain68] ___________ [gw5] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', 'same'), method_chain = ('overlap', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('overlap', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:145 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 E (and 27 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ___________ test_three_in_a_row[strandedness_chain64-method_chain64] ___________ [gw9] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', 'same') method_chain = ('overlap', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('overlap', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:145 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 E (and 27 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') _________________ test_k_nearest[downstream-False-False-last] __________________ [gw3] linux -- Python 3.12.6 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 880, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 510, in test_k_nearest | @pytest.mark.explore | ^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1722, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 548, in test_k_nearest | result = gr.k_nearest( | ^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2450, in k_nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 292, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 180, in _nearest | df = __nearest(d1, d2, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 115, in nearest_previous | lidx, ridx, dist = nearest_previous_idx(d1, d2, d1.__k__.values, ties) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 28, in nearest_previous_idx | lidx, ridx_pos, dist = k_nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/k_nearest.pyx", line 28, in sorted_nearest.src.k_nearest.k_nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_k_nearest( | nearest_how='downstream', | overlap=False, | strandedness=False, | ties='last', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:14 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:15 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:160 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:171 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:19 | (and 36 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2TAAIyMmGIMAAB5AAQ=') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 548, in test_k_nearest | result = gr.k_nearest( | ^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2450, in k_nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 292, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 180, in _nearest | df = __nearest(d1, d2, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 140, in nearest_next | lidx, ridx, dist = nearest_next_idx(d1, d2, d1.__k__.values, ties) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 56, in nearest_next_idx | lidx, ridx_pos, dist = k_nearest_next_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/k_nearest.pyx", line 55, in sorted_nearest.src.k_nearest.k_nearest_next_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_k_nearest( | nearest_how='downstream', | overlap=False, | strandedness=False, | ties='last', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:160 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:171 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:41 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:42 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:46 | (and 37 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2TABIxYxAAAZAAD') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkak675gu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkak675gu/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmppe6ceayy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppe6ceayy/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6ha4meuk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6ha4meuk/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpp4ie4x0y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp4ie4x0y/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmppm54rv1e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppm54rv1e/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7hh1sj9t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7hh1sj9t/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpq9kinap9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq9kinap9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzj7gkss0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzj7gkss0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0sx47xd5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0sx47xd5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpli7erszl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpli7erszl/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpo_4a0ekh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo_4a0ekh/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpq2ezfd27/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq2ezfd27/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbs028e5p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbs028e5p/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzjq0f98w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzjq0f98w/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmph_ozsu5i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph_ozsu5i/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpf0fz1u49/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf0fz1u49/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4te9pg84/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4te9pg84/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpu67ylcbr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu67ylcbr/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6uk9pigc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6uk9pigc/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpm6u87kfl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm6u87kfl/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmphhgdsh83/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphhgdsh83/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmprh3x9g5z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprh3x9g5z/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjx_hrq3w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjx_hrq3w/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9twvt4i_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9twvt4i_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuhszp60u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuhszp60u/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpr97yy4za/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr97yy4za/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpq_jjdt1o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq_jjdt1o/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvtrvvyus/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvtrvvyus/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpe4oomkah/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe4oomkah/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpb5k82klq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb5k82klq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpei2wtr0u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpei2wtr0u/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpaxxl6ysl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaxxl6ysl/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp710f_5w9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp710f_5w9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnmkdoimu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnmkdoimu/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmplc8759ed/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplc8759ed/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpf184t7y3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf184t7y3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjjq1olf9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjjq1olf9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9jbsxd_l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9jbsxd_l/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmps72o9xtu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps72o9xtu/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6q8i4sx9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6q8i4sx9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcgyqlwdw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcgyqlwdw/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzjepunxx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzjepunxx/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpz9fe5w6r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz9fe5w6r/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5l7zc1a5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5l7zc1a5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvtqf23fx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvtqf23fx/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpru_6dwfi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpru_6dwfi/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpl6anv400/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl6anv400/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpiqfi6fh8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiqfi6fh8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpo0a4k3cy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo0a4k3cy/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4z7hcbqs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4z7hcbqs/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjml0qdqo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjml0qdqo/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_ymthzoy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_ymthzoy/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnbhti91p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnbhti91p/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpk83_pba9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk83_pba9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7oq8dqdb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7oq8dqdb/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzbyab_ot/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzbyab_ot/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxm1jmg70/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxm1jmg70/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7jxrmnzu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7jxrmnzu/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmprobqjceh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprobqjceh/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmt8s1eil/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmt8s1eil/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpoayugvf2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoayugvf2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpll4kxgvo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpll4kxgvo/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcr80nkf8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcr80nkf8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1u4_2vhc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1u4_2vhc/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9xav985r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9xav985r/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6kc_3x_x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6kc_3x_x/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdc4ejo_a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdc4ejo_a/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2q5etj41/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2q5etj41/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_l87vxyq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_l87vxyq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpf0e2z9ka/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf0e2z9ka/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7jsu7ux_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7jsu7ux_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpa3o4ux47/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa3o4ux47/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpaznsfceb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaznsfceb/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpj3mhptvz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj3mhptvz/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp00_t1hmv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp00_t1hmv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8slmueoc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8slmueoc/f2.bed) ----------------------------- Captured stderr call ----------------------------- Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. ___________ test_three_in_a_row[strandedness_chain15-method_chain15] ___________ [gw7] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', False) method_chain = ('overlap', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('overlap', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:15 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:145 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:369 E (and 23 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ___________ test_three_in_a_row[strandedness_chain39-method_chain39] ___________ [gw8] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', False), method_chain = ('subtract', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('subtract', 'intersect'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:30 E /usr/lib/python3/dist-packages/pandas/core/dtypes/missing.py:207 E (and 18 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ___________ test_three_in_a_row[strandedness_chain53-method_chain53] ___________ [gw10] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', 'same'), method_chain = ('set_union', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('set_union', 'intersect'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E (and 184 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2CAA0YGLAAAADUAAg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 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'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') _____________________ test_nearest[downstream-False-False] _____________________ [gw2] linux -- Python 3.12.6 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 880, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 323, in test_nearest | @pytest.mark.parametrize("nearest_how,overlap,strandedness", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1722, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 351, in test_nearest | result = gr.nearest( | ^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 292, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 118, in _nearest | r_idx, dist = _previous_nonoverlapping(df_to_find_nearest_in.Start, | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_nearest( | nearest_how='downstream', | overlap=False, | strandedness=False, | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:101 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:118 | (and 40 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2TAAIyMmGIMAAB5AAQ=') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 351, in test_nearest | result = gr.nearest( | ^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 292, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 115, in _nearest | r_idx, dist = _next_nonoverlapping(df_to_find_nearest_in.End, | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 62, in _next_nonoverlapping | r_idx, dist = nearest_next_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 34, in sorted_nearest.src.sorted_nearest.nearest_next_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_nearest( | nearest_how='downstream', | overlap=False, | strandedness=False, | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:101 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:115 | (and 40 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2TABIxYxAAAZAAD') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpm_y2qxhz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm_y2qxhz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplhscnsd2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplhscnsd2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprreu0s3o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprreu0s3o/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprs04hh1a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprs04hh1a/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdcdtca8k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdcdtca8k/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpav640db7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpav640db7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdy53xtqm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdy53xtqm/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpoug3a_b6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoug3a_b6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptp5edom6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptp5edom6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppy3qcsfr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppy3qcsfr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp60pk4lb6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp60pk4lb6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgvru174m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgvru174m/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4ka98_2k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4ka98_2k/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1qx4blxf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1qx4blxf/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpej__qdhl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpej__qdhl/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgqif6sb7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgqif6sb7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8o_fu20j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8o_fu20j/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_mjgljfy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_mjgljfy/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_zex8c58/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_zex8c58/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplq5jalr1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplq5jalr1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6oupeyku/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6oupeyku/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbatdyh_m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbatdyh_m/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxcjffyo7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxcjffyo7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplbei3vde/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplbei3vde/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkq0t2ni8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkq0t2ni8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprzg3328m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprzg3328m/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmu37ei9r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmu37ei9r/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvsv0fvh3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvsv0fvh3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmph23fhur4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph23fhur4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplo4z6170/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplo4z6170/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe4jhdrud/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe4jhdrud/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpesg6d2by/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpesg6d2by/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpeflg_em7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpeflg_em7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7p86go2_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7p86go2_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjwjesxk6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjwjesxk6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvo03b8u_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvo03b8u_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplupi3ftj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplupi3ftj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpf8bq2le8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf8bq2le8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_ve9mi_o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_ve9mi_o/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp__59yywg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp__59yywg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqkbb2p1z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqkbb2p1z/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdrg4e52z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdrg4e52z/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpg61degfw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg61degfw/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbsazzt_p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbsazzt_p/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpeergoel1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpeergoel1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzwo3140u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzwo3140u/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp82qa7mou/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp82qa7mou/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsen66kvm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsen66kvm/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpj8e8lkx5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj8e8lkx5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpj1e8iukv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj1e8iukv/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpu7212fzr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu7212fzr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp44l34ynb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp44l34ynb/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpazs31fiv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpazs31fiv/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplt083tx7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplt083tx7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprc6967zz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprc6967zz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvmz_k8wa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvmz_k8wa/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpx3hrxzfr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx3hrxzfr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8yxd17u3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8yxd17u3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdq6tgqb4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdq6tgqb4/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpoby1hw1e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoby1hw1e/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpboc3a3nc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpboc3a3nc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpv9tbuxrw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv9tbuxrw/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5xonaoqa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5xonaoqa/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_2x5dy_w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_2x5dy_w/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjc7mmwt4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjc7mmwt4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfvtzcz5_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfvtzcz5_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyzrzy3ce/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyzrzy3ce/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4bpyqm14/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4bpyqm14/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwjpxdxyl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwjpxdxyl/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmv5rod7k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmv5rod7k/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpne_8amr9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpne_8amr9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppn8llcon/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppn8llcon/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpul2r_fq6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpul2r_fq6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbk1htl8x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbk1htl8x/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpile_twu0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpile_twu0/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpu1npyijw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu1npyijw/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1prbt888/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1prbt888/f2.bed) ___________ test_three_in_a_row[strandedness_chain80-method_chain80] ___________ [gw4] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', 'same'), method_chain = ('intersect', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('intersect', 'nearest'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E | chr1 | 1 | 2 | a | 0 | + | E | chr1 | 1 | 2 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:73 E (and 27 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2QAAUYgBCEwhnAZQSKMTGBe/sxlUDVQBRA1KHy4MQyMAFG5Acc=') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 890016 | 896897 | a | 0 | ... | | chr1 | 5217264 | 5226095 | a | 0 | ... | | chr1 | 6017732 | 6021997 | a | 0 | ... | | chr1 | 3366576 | 3368729 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 9001601 | 9010535 | a | 0 | ... | | chr1 | 2934347 | 2941041 | a | 0 | ... | | chr1 | 3677156 | 3686186 | a | 0 | ... | | chr12 | 1275222 | 1281452 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 8485624 | 8488689 | a | 0 | ... | | chr1 | 8485624 | 8488689 | a | 0 | ... | | chr1 | 8485624 | 8488689 | a | 0 | ... | | chr1 | 6534319 | 6539853 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 8485624 | 8488689 | a | 0 | ... | | chr1 | 3810514 | 3812543 | a | 0 | ... | | chr1 | 8485624 | 8487225 | a | 0 | ... | | chr1 | 3047636 | 3054548 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 16 rows and 12 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 4 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 4 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 4 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. _________________________ test_nearest[None-True-same] _________________________ [gw1] linux -- Python 3.12.6 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 880, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 323, in test_nearest | @pytest.mark.parametrize("nearest_how,overlap,strandedness", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1722, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 351, in test_nearest | result = gr.nearest( | ^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_nearest( | nearest_how=None, | overlap=True, | strandedness='same', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | (and 126 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2TABIxYOAAAawAE') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 359, in test_nearest | compare_results_nearest(bedtools_df, result) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 107, in compare_results_nearest | assert_df_equal(result_df, bedtools_df) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/helpers.py", line 60, in assert_df_equal | pd.testing.assert_frame_equal(df1, df2) | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 1279, in assert_frame_equal | assert_series_equal( | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 975, in assert_series_equal | assert_attr_equal("dtype", left, right, obj=f"Attributes of {obj}") | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 421, in assert_attr_equal | raise_assert_detail(obj, msg, left_attr, right_attr) | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 614, in raise_assert_detail | raise AssertionError(msg) | AssertionError: Attributes of DataFrame.iloc[:, 4] (column name="Distance") are different | | Attribute "dtype" are different | [left]: int32 | [right]: int64 | Falsifying example: test_nearest( | nearest_how=None, | overlap=True, | strandedness='same', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | (and 463 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2TABIxYxAAAZAAD') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuawip2ar/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuawip2ar/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe20p9gin/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe20p9gin/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpa5un1ckk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa5un1ckk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpr8jyzrrg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr8jyzrrg/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1126554 1131396 - 0 1 chr1 4510431 4511535 - 0 2 chr1 5803999 5804256 - 0 3 chr1 6496619 6498527 + 0 4 chr11 5712108 5712365 - 0 5 chr7 2 259 - 0 6 chr7 1126554 1134877 - 0 7 chr7 8961960 8971499 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 6496619 | 6498527 | a | 0 | ... | | chr1 | 1126554 | 1131396 | a | 0 | ... | | chr1 | 5803999 | 5804256 | a | 0 | ... | | chr1 | 4510431 | 4511535 | a | 0 | ... | | chr7 | 8961960 | 8971499 | a | 0 | ... | | chr7 | 2 | 259 | a | 0 | ... | | chr7 | 1126554 | 1134877 | a | 0 | ... | | chr11 | 5712108 | 5712365 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 8 rows and 12 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 5 chr7 2 259 - 0 1 chr1 1126554 1131396 - 0 6 chr7 1126554 1134877 - 0 3 chr1 4510431 4511535 - 0 7 chr11 5712108 5712365 - 0 2 chr1 5803999 5804256 - 0 0 chr1 6496619 6498527 + 0 4 chr7 8961960 8971499 - 0 df2 Chromosome Start End Strand Distance 5 chr7 2 259 - 0 0 chr1 1126554 1131396 - 0 6 chr7 1126554 1134877 - 0 1 chr1 4510431 4511535 - 0 4 chr11 5712108 5712365 - 0 2 chr1 5803999 5804256 - 0 3 chr1 6496619 6498527 + 0 7 chr7 8961960 8971499 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1126554 1131396 - 0 1 chr1 4510431 4511535 - 0 2 chr1 5803999 5804256 - 0 3 chr1 6496619 6498527 + 0 4 chr11 5712108 5712365 - 0 5 chr7 2 259 - 0 6 chr7 1126554 1134877 - 0 7 chr7 8961960 8971499 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1126554 1131396 - 0 1 chr1 4510431 4511535 - 0 2 chr1 5803999 5804256 - 0 3 chr1 6496619 6498527 + 0 4 chr11 5712108 5712365 - 0 5 chr7 2 259 - 0 6 chr7 1126554 1134877 - 0 7 chr7 8961960 8971499 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=8, step=1) Expected index RangeIndex(start=0, stop=8, step=1) index equal [ True True True True True True True True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpeewh5syt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpeewh5syt/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1126554 1131396 - 0 1 chr1 4510431 4511535 - 0 2 chr1 5803999 5804256 - 0 4 chr11 5712108 5712365 - 0 5 chr7 2 259 - 0 6 chr7 1126554 1134877 - 0 7 chr7 8961960 8971499 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1126554 | 1131396 | a | 0 | ... | | chr1 | 5803999 | 5804256 | a | 0 | ... | | chr1 | 4510431 | 4511535 | a | 0 | ... | | chr7 | 8961960 | 8971499 | a | 0 | ... | | chr7 | 2 | 259 | a | 0 | ... | | chr7 | 1126554 | 1134877 | a | 0 | ... | | chr11 | 5712108 | 5712365 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 7 rows and 12 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 4 chr7 2 259 - 0 0 chr1 1126554 1131396 - 0 5 chr7 1126554 1134877 - 0 2 chr1 4510431 4511535 - 0 6 chr11 5712108 5712365 - 0 1 chr1 5803999 5804256 - 0 3 chr7 8961960 8971499 - 0 df2 Chromosome Start End Strand Distance 5 chr7 2 259 - 0 0 chr1 1126554 1131396 - 0 6 chr7 1126554 1134877 - 0 1 chr1 4510431 4511535 - 0 4 chr11 5712108 5712365 - 0 2 chr1 5803999 5804256 - 0 7 chr7 8961960 8971499 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1126554 1131396 - 0 1 chr1 4510431 4511535 - 0 2 chr1 5803999 5804256 - 0 3 chr11 5712108 5712365 - 0 4 chr7 2 259 - 0 5 chr7 1126554 1134877 - 0 6 chr7 8961960 8971499 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1126554 1131396 - 0 1 chr1 4510431 4511535 - 0 2 chr1 5803999 5804256 - 0 3 chr11 5712108 5712365 - 0 4 chr7 2 259 - 0 5 chr7 1126554 1134877 - 0 6 chr7 8961960 8971499 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=7, step=1) Expected index RangeIndex(start=0, stop=7, step=1) index equal [ True True True True True True True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpanyyawcn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpanyyawcn/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsnctbdsi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsnctbdsi/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7_473x4a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7_473x4a/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptucf34x8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptucf34x8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpp1cqc3hs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp1cqc3hs/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpu0lm16pb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu0lm16pb/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkwb3mlxz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkwb3mlxz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7p2fmi71/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7p2fmi71/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6nzyjaxl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6nzyjaxl/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpabqj4oop/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpabqj4oop/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmiu2jca4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmiu2jca4/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvr04mjnd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvr04mjnd/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpz9_nge4d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz9_nge4d/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwaev7bpw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwaev7bpw/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpf15gl62h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf15gl62h/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpu70kvaou/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu70kvaou/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_f4pz198/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_f4pz198/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpc8l1wwq3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc8l1wwq3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpx7g9wz5g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx7g9wz5g/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpg5tykr_8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg5tykr_8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp652lhzs8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp652lhzs8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvah9ecjz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvah9ecjz/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxh__efp9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxh__efp9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpv2sf358k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv2sf358k/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpswkp28nk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpswkp28nk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7q_ffu_4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7q_ffu_4/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 258 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 258 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 1 2 + 0 0 chr1 1 258 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 258 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 258 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 258 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmgx7sl9_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmgx7sl9_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4q1ckrcy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4q1ckrcy/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpm98nq7f8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm98nq7f8/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsio6stal/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsio6stal/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpasfshvhj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpasfshvhj/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 258 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 258 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 1 2 + 0 0 chr1 1 258 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 258 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 258 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 258 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpx6aw973v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx6aw973v/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpz7qyiw6r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz7qyiw6r/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp90g5z2rq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp90g5z2rq/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzhgniv2i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzhgniv2i/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprq5n_k0b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprq5n_k0b/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppaq1aps5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppaq1aps5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyceis4ws/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyceis4ws/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfj803e5o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfj803e5o/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmx7padcf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmx7padcf/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe7414ufp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe7414ufp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp41m4ai01/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp41m4ai01/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_6fmq9p2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_6fmq9p2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpufb92xpd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpufb92xpd/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpchgldg4g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpchgldg4g/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpq6j2l1k3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq6j2l1k3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzxpg5vh1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzxpg5vh1/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfdar9vgu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfdar9vgu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmpbyd_p4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmpbyd_p4/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_ooafhli/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_ooafhli/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjd0kywy2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjd0kywy2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpw5jh7dvo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw5jh7dvo/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp35cdezyj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp35cdezyj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7_ydz26h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7_ydz26h/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpo7gojz7c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo7gojz7c/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp58i2s4vo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp58i2s4vo/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpovyk_ryn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpovyk_ryn/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_tkbfi08/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_tkbfi08/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxgzg18ej/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxgzg18ej/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6yvvm377/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6yvvm377/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_ia_ctcq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_ia_ctcq/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyujc09zj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyujc09zj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjc7f5zxp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjc7f5zxp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3stldyoj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3stldyoj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplaqn5oc0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplaqn5oc0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp11s4unm7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp11s4unm7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqdcix_kr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqdcix_kr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpk318efqc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk318efqc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpj69z1tr5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj69z1tr5/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpggb7mca3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpggb7mca3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyr757zb6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyr757zb6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2_p2zmw0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2_p2zmw0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4dzfm23_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4dzfm23_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0xf99_q6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0xf99_q6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1qzylya7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1qzylya7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqvaa_k4m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqvaa_k4m/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuu2nr42z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuu2nr42z/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6ciy7xus/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6ciy7xus/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpshb22nh5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpshb22nh5/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpf6wof3je/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf6wof3je/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwy7abb24/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwy7abb24/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcrp86z8e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcrp86z8e/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7ta6hmgi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7ta6hmgi/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 3 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 3 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 3 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 3 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 3 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9nwk7os0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9nwk7os0/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkgghbiv4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkgghbiv4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpt3fjxdhk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt3fjxdhk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8pr70oj8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8pr70oj8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp61ux7wy0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp61ux7wy0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpc5nntbe6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc5nntbe6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpm7az9ooy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm7az9ooy/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmps62rc_95/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps62rc_95/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2pb50t9h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2pb50t9h/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpt41_pcpj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt41_pcpj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpy3chfzjs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy3chfzjs/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqoqelnqn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqoqelnqn/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpj3sjp0wa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj3sjp0wa/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpni4qhj1m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpni4qhj1m/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppg7id5ej/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppg7id5ej/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvkuo8zm4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvkuo8zm4/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpy4w3qad8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy4w3qad8/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 3 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 3 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 3 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 3 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 3 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppe4cssvz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppe4cssvz/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpref3xlvg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpref3xlvg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5w2g586n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5w2g586n/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpl6bq4ov6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl6bq4ov6/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwfq0w0i3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwfq0w0i3/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplz13xprw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplz13xprw/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpk1gb3q3f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk1gb3q3f/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpeyxq0qkv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpeyxq0qkv/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp44z6xb8f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp44z6xb8f/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpytggo78t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpytggo78t/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwwu5bk0j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwwu5bk0j/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ________________ test_k_nearest[downstream-True-opposite-last] _________________ [gw3] linux -- Python 3.12.6 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 880, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 510, in test_k_nearest | @pytest.mark.explore | ^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1722, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 548, in test_k_nearest | result = gr.k_nearest( | ^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2450, in k_nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 180, in _nearest | df = __nearest(d1, d2, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 115, in nearest_previous | lidx, ridx, dist = nearest_previous_idx(d1, d2, d1.__k__.values, ties) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 28, in nearest_previous_idx | lidx, ridx_pos, dist = k_nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/k_nearest.pyx", line 28, in sorted_nearest.src.k_nearest.k_nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_k_nearest( | nearest_how='downstream', | overlap=True, | strandedness='opposite', | ties='last', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:14 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:15 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:160 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:171 | (and 40 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2QAA0YGOGBkxBBiAAAAngAG') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 548, in test_k_nearest | result = gr.k_nearest( | ^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2450, in k_nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 180, in _nearest | df = __nearest(d1, d2, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 140, in nearest_next | lidx, ridx, dist = nearest_next_idx(d1, d2, d1.__k__.values, ties) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 56, in nearest_next_idx | lidx, ridx_pos, dist = k_nearest_next_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/k_nearest.pyx", line 55, in sorted_nearest.src.k_nearest.k_nearest_next_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_k_nearest( | nearest_how='downstream', | overlap=True, | strandedness='opposite', | ties='last', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:160 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:171 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:41 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:42 | (and 41 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2QAA0YGBGDEEGIEAACLAAY=') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgowc2j5o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgowc2j5o/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcv1or7p2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcv1or7p2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkzz9ax5t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkzz9ax5t/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9_k13p29/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9_k13p29/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvb_1kt02/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvb_1kt02/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5r_nnlz2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5r_nnlz2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpiudw5zv0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiudw5zv0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3nbm0l7z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3nbm0l7z/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjzsxbt1a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjzsxbt1a/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmputjrpww1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmputjrpww1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpf4wl8df0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf4wl8df0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4bsrxx9x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4bsrxx9x/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpybekmaco/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpybekmaco/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpj0415fav/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj0415fav/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmprxqsyer8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprxqsyer8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuniq0sch/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuniq0sch/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvmo8x47d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvmo8x47d/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpndjkmpw3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpndjkmpw3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpv38dbh7e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv38dbh7e/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2krapc71/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2krapc71/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpx_oo8kgs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx_oo8kgs/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgm7uvj78/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgm7uvj78/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpz58pvvrv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz58pvvrv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8b_78b10/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8b_78b10/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7mxsacd_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7mxsacd_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5uys0h9y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5uys0h9y/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpj8bte468/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj8bte468/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqcxuubcv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqcxuubcv/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpa403rwyw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa403rwyw/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6sxu_7t_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6sxu_7t_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpi0cycz4_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi0cycz4_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpogydwafz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpogydwafz/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpo_5a7b3q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo_5a7b3q/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7dv7tz6t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7dv7tz6t/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpujsykfy8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpujsykfy8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmph1fel3aq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph1fel3aq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpa3jnfim3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa3jnfim3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8cx8gw8s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8cx8gw8s/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7yxikukz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7yxikukz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmps0n6m0l8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps0n6m0l8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmphtpkvg6p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphtpkvg6p/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsv4sfzhf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsv4sfzhf/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpv98u9mln/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv98u9mln/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsoz6_g63/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsoz6_g63/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6yfrtxxx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6yfrtxxx/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpu6hxz5o0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu6hxz5o0/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmphdqfz_nx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphdqfz_nx/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjxsrpyex/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjxsrpyex/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmprovcewzj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprovcewzj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpz_dm4xh6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz_dm4xh6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmppedwrsot/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppedwrsot/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpslaus6kd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpslaus6kd/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdxl2ofqm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdxl2ofqm/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfj1vbkbu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfj1vbkbu/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpu1nmnxer/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu1nmnxer/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8pe0260g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8pe0260g/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmph35j61kz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph35j61kz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgaom8kpn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgaom8kpn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4cyvgt5_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4cyvgt5_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6irdzxhi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6irdzxhi/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5f_t203r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5f_t203r/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1fpqgz42/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1fpqgz42/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdfreccr3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdfreccr3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpro8v57qu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpro8v57qu/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8t1q77qx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8t1q77qx/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8pqjgkl6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8pqjgkl6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_7rjaro4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_7rjaro4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpf0o804mf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf0o804mf/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6qkz7vb6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6qkz7vb6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5rg6vc0i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5rg6vc0i/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6krodqcz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6krodqcz/f2.bed) ----------------------------- Captured stderr call ----------------------------- Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain26-method_chain26] ___________ [gw6] linux -- Python 3.12.6 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 880, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1722, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', False), | method_chain=('nearest', 'subtract'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 5585468 | 5585470 | a | 0 | - | | | chr1 | 1 | 2 | a | 0 | - | | | chr1 | 1882410 | 1882414 | a | 0 | - | | | chr6 | 3 | 4 | a | 0 | - | | | chr21 | 3 | 6 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 5 rows and 6 columns from 3 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 75 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr16 | 65537 | 65539 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:73 | (and 28 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY8ztdUxjdOQ7N5cxIDOtgNFV6tdXRiWtfTkMjEDAwiDCyMLIBGQAOcwMrCAxRmZGBiBkYWRgYAKxgSSDc6iVNSOTk8xOTbByBiAGyQHVAHUxMzAwgBWC+ECzQCxGsBlgAFIMVAPjQoRAYgwMYEUMYABieEIEHMDmgQiIGhDBBFHDwA8kihBaQRAAH0AMyA==') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 4384, in subtract | other_clusters = other.merge(strand=strand) | ^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 381, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', False), | method_chain=('nearest', 'subtract'), | gr=Empty PyRanges, | gr2=Empty PyRanges, | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:15 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:369 | (and 24 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 75 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 75 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain40-method_chain40] ___________ [gw8] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', False), method_chain = ('subtract', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('subtract', 'subtract'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:30 E (and 19 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 569517 | 572376 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr2 | 1 | 2 | a | 0 | + | | chr2 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________________ test_k_nearest[downstream-True-same-last] ___________________ [gw3] linux -- Python 3.12.6 /usr/bin/python3.12 nearest_how = 'downstream', overlap = True, strandedness = 'same', ties = 'last' @pytest.mark.bedtools > @pytest.mark.explore tests/test_binary.py:510: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:548: in test_k_nearest result = gr.k_nearest( pyranges/pyranges.py:2450: in k_nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/k_nearest.py:180: in _nearest df = __nearest(d1, d2, **kwargs) pyranges/methods/k_nearest.py:140: in nearest_next lidx, ridx, dist = nearest_next_idx(d1, d2, d1.__k__.values, ties) pyranges/methods/k_nearest.py:56: in nearest_next_idx lidx, ridx_pos, dist = k_nearest_next_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_k_nearest( E nearest_how='downstream', E overlap=True, E strandedness='same', E ties='last', E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:160 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:171 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:41 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:42 E (and 41 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2TABIxYxAAAZAAD') as a decorator on your test case sorted_nearest/src/k_nearest.pyx:55: ValueError ----------------------------- Captured stdout call ----------------------------- ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp11d8w212/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp11d8w212/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0egvrg4i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0egvrg4i/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpno9rcata/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpno9rcata/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpg_yaz834/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg_yaz834/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcas_q8jo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcas_q8jo/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpd676nl7x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd676nl7x/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_7ilmd3u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_7ilmd3u/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9fnyxfo0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9fnyxfo0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp77ksg25s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp77ksg25s/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7d3ddfuj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7d3ddfuj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8d208cln/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8d208cln/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1as44qeb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1as44qeb/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfidvt38w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfidvt38w/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9knh7big/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9knh7big/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpef0zfzj5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpef0zfzj5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpydzlug_i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpydzlug_i/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgk66qh6v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgk66qh6v/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpps2pvhlw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpps2pvhlw/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5s77gsci/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5s77gsci/f2.bed) ----------------------------- Captured stderr call ----------------------------- Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr21 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr21 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. ___________ test_three_in_a_row[strandedness_chain17-method_chain17] ___________ [gw7] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', False), method_chain = ('overlap', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:292: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('overlap', 'nearest'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | + | E | chr1 | 2 | 3 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | + | E | chr1 | 2 | 3 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:53 E (and 29 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2RgYGBkZAADMMWIREKEoGxGBqgYTAlMA5JmKAAABBYAFA==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain70-method_chain70] ___________ [gw5] linux -- Python 3.12.6 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 880, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1722, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', 'same'), | method_chain=('nearest', 'set_union'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 7281075 | 7290684 | a | 0 | + | | | chr1 | 5136923 | 5138800 | a | 0 | + | | | chr1 | 10000000 | 10001947 | a | 0 | + | | | chr1 | 2 | 9499 | a | 0 | + | | | ... | ... | ... | ... | ... | ... | | | chr1 | 2 | 9499 | a | 0 | + | | | chr1 | 4082539 | 4087594 | a | 0 | - | | | chr1 | 2 | 2374 | a | 0 | - | | | chr1 | 7039535 | 7042655 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 10 rows and 6 columns from 4 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 65559 | 68998 | a | 0 | - | | | chr21 | 9999999 | 10004151 | a | 0 | + | | | chr21 | 1 | 8713 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 3 rows and 6 columns from 2 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr17 | 3119839 | 3123820 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | (and 170 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicLVC7SkNBFDyz9+59gJKHJkYhFpFooSQQFQvhNqJBfAW1CARRYvARQVFJ4yMhnYWNTQwpbQULwdbOL7AIWsQy/kA6Ec9uZNmdw9nZmTkL7+J9GSOj1TeM3T1l4EVyH5jIda4hxxP3WMu3JJzqSxPR9VQKK9n2L8EFLIpAUIBLB7ABIuLDp8r/TTC6IGDyFTMNWLwNblpMRjbQ/IIoFTOfiuKdDD4zUsFbKjIaZSVoX9VrFTiho2JC9VhF7q3mhyD5uVTOcDUPbOEww2EXCZPSsc4w7F27AZm2NyES4R84mZ4kaKfvVbEO4xEW46Ab0SlYB8EBbpqL8RtOaGpdkytuqdQFd470AOzO05D2lmo6C4rLDQEFJnUj6pktvQSnCwW/p7Hte5jHfrSdV8+J+oEzUBh0qT5OLSVAVKnXyqCFGCc77z2GcP0z+lKQFlWk2dPSo6L6+dhKNloMk75bLfIHSZ03Kg==') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3784, in set_union | gr = gr.merge(strand=strand) | ^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 347, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', 'same'), | method_chain=('nearest', 'set_union'), | gr=Empty PyRanges, | gr2=Empty PyRanges, | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 | (and 222 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain54-method_chain54] ___________ [gw10] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', 'same'), method_chain = ('set_union', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('set_union', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E /usr/lib/python3/dist-packages/natsort/utils.py:344 E (and 119 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkcvjxSFvFioGBkQETAABFcAKo') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. _____________________ test_nearest[downstream-False-same] ______________________ [gw2] linux -- Python 3.12.6 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 880, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 323, in test_nearest | @pytest.mark.parametrize("nearest_how,overlap,strandedness", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1722, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 351, in test_nearest | result = gr.nearest( | ^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 115, in _nearest | r_idx, dist = _next_nonoverlapping(df_to_find_nearest_in.End, | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 62, in _next_nonoverlapping | r_idx, dist = nearest_next_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 34, in sorted_nearest.src.sorted_nearest.nearest_next_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_nearest( | nearest_how='downstream', | overlap=False, | strandedness='same', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | (and 103 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2TABIxYxAAAZAAD') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 351, in test_nearest | result = gr.nearest( | ^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 118, in _nearest | r_idx, dist = _previous_nonoverlapping(df_to_find_nearest_in.Start, | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_nearest( | nearest_how='downstream', | overlap=False, | strandedness='same', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | (and 103 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2QAA0YGOGBkxBQCAACfAAc=') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpquw1z95b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpquw1z95b/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdv01ofzn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdv01ofzn/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplqxuw4lb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplqxuw4lb/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgpbqi5w0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgpbqi5w0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnijowyfa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnijowyfa/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpndzpsh3u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpndzpsh3u/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpihtnas1g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpihtnas1g/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnovauzhi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnovauzhi/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmaxox2nw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmaxox2nw/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4m7fq8q6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4m7fq8q6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjvp4dbie/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjvp4dbie/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpl99zgkc5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl99zgkc5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp00e6k0i1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp00e6k0i1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnuo56oq1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnuo56oq1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7rmmycqa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7rmmycqa/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp92ibto_h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp92ibto_h/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptimer02y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptimer02y/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpz20ttant/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz20ttant/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmps35szrkf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps35szrkf/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_hg6uwcz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_hg6uwcz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4arfzfsc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4arfzfsc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpko3w0nht/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpko3w0nht/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsf7mde_o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsf7mde_o/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpj4f6du1j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj4f6du1j/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpj4zp72ge/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj4zp72ge/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_33q6wq5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_33q6wq5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjbd24buh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjbd24buh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9jr3ng68/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9jr3ng68/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpldt841ql/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpldt841ql/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdf6z0ybw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdf6z0ybw/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6y1mzboi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6y1mzboi/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpr1c3r6b7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr1c3r6b7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp831z3uzl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp831z3uzl/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7x_6iq34/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7x_6iq34/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphlsq95ng/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphlsq95ng/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnet4pyg2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnet4pyg2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7q493lh3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7q493lh3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpi7159thm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi7159thm/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8cnic3j1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8cnic3j1/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpx9xaco1u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx9xaco1u/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp25ockj4z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp25ockj4z/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgrj8mair/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgrj8mair/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzmoix50f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzmoix50f/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqp_b4ffg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqp_b4ffg/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5onj948e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5onj948e/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7vyrwfss/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7vyrwfss/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_2b5z54q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_2b5z54q/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzrpmskg7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzrpmskg7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpun0n3z3l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpun0n3z3l/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdzu8c3hf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdzu8c3hf/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwm1d2oeh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwm1d2oeh/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6iug98js/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6iug98js/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp08_fkvgo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp08_fkvgo/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpchr4j20o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpchr4j20o/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpku29k50c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpku29k50c/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6sgqctg5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6sgqctg5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8kxcq770/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8kxcq770/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpl30h9vi1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl30h9vi1/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpr292d4mu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr292d4mu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9xash30j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9xash30j/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpq9tgktn5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq9tgktn5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbt3d4tz8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbt3d4tz8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpo5rmdrdy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo5rmdrdy/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjx8w9fai/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjx8w9fai/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp22kcugqh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp22kcugqh/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp74xup3qe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp74xup3qe/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpouj4ecff/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpouj4ecff/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpy8ceintk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy8ceintk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpg6h9eaq1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg6h9eaq1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwco3ijsv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwco3ijsv/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphxsxelc_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphxsxelc_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwjb9b_k6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwjb9b_k6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpy_1za5yw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy_1za5yw/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3rtul3g3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3rtul3g3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpaqoi85q1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaqoi85q1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2_9eh5m5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2_9eh5m5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1i80620g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1i80620g/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp40r8m1gp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp40r8m1gp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4xuqnc2i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4xuqnc2i/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuc68irnx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuc68irnx/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4mfmcvdb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4mfmcvdb/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3pssqakg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3pssqakg/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2qlq7oi_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2qlq7oi_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpp46w73xd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp46w73xd/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdwgthset/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdwgthset/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyiad_q5i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyiad_q5i/f2.bed) ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain66-method_chain66] ___________ [gw9] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', 'same'), method_chain = ('overlap', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('overlap', 'nearest'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 258 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | - | E | chr1 | 1 | 2 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:110 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E (and 28 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2QAAUYghCBGEI+RESEK4sKEGJkgglAJCGAEAAOBABk=') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chrY | 1161059 | 1163676 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 8949604 | 8959604 | a | 0 | ... | | chr1 | 1263906 | 1269180 | a | 0 | ... | | chr1 | 1263906 | 1263993 | a | 0 | ... | | chr1 | 1263906 | 1266485 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr6 | 8654776 | 8663054 | a | 0 | ... | | chr8 | 1279291 | 1288571 | a | 0 | ... | | chr17 | 1263906 | 1269801 | a | 0 | ... | | chrX | 5701362 | 5709588 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 10 rows and 12 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 6100180 | 6100181 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 258 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain82-method_chain82] ___________ [gw4] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', 'same'), method_chain = ('intersect', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('intersect', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:145 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 E /usr/lib/python3/dist-packages/pandas/core/dtypes/missing.py:207 E (and 18 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. _______________________ test_nearest[None-True-opposite] _______________________ [gw1] linux -- Python 3.12.6 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 880, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 323, in test_nearest | @pytest.mark.parametrize("nearest_how,overlap,strandedness", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1722, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 351, in test_nearest | result = gr.nearest( | ^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_nearest( | nearest_how=None, | overlap=True, | strandedness='opposite', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | (and 126 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2RAAowQkhGZBwEAAJsABg==') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 359, in test_nearest | compare_results_nearest(bedtools_df, result) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 107, in compare_results_nearest | assert_df_equal(result_df, bedtools_df) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/helpers.py", line 60, in assert_df_equal | pd.testing.assert_frame_equal(df1, df2) | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 1279, in assert_frame_equal | assert_series_equal( | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 975, in assert_series_equal | assert_attr_equal("dtype", left, right, obj=f"Attributes of {obj}") | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 421, in assert_attr_equal | raise_assert_detail(obj, msg, left_attr, right_attr) | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 614, in raise_assert_detail | raise AssertionError(msg) | AssertionError: Attributes of DataFrame.iloc[:, 4] (column name="Distance") are different | | Attribute "dtype" are different | [left]: int32 | [right]: int64 | Falsifying example: test_nearest( | nearest_how=None, | overlap=True, | strandedness='opposite', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | (and 457 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2TAAIyMUBpJDAAAgQAF') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpemx2fi_9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpemx2fi_9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpw37tcg7o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw37tcg7o/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpntw3eco2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpntw3eco2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplvnpadch/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplvnpadch/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprxvzs05a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprxvzs05a/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpf5vq6dse/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf5vq6dse/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpa5kt0fo6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa5kt0fo6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpulg8at9k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpulg8at9k/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxeavdjqm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxeavdjqm/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpc546tlsr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc546tlsr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4sfxv497/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4sfxv497/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpg20m6xc9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg20m6xc9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvrky4xrl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvrky4xrl/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpce8nsxtw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpce8nsxtw/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0mlu7o_l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0mlu7o_l/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwdwplm10/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwdwplm10/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_63qo3qi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_63qo3qi/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdcuz71uf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdcuz71uf/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpudgz4jjw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpudgz4jjw/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprrt_5d5b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprrt_5d5b/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplv_93qvv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplv_93qvv/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6b6hv2oe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6b6hv2oe/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9ccbccbc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9ccbccbc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpesctif5d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpesctif5d/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdu8y3g24/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdu8y3g24/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp23w2kpq9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp23w2kpq9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprnnn036o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprnnn036o/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpaveis4er/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaveis4er/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9qhbizxg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9qhbizxg/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpx4x78exs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx4x78exs/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6irgq87a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6irgq87a/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplc_yarud/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplc_yarud/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpclcvhxcj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpclcvhxcj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1o6v37ny/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1o6v37ny/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3v76cmt9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3v76cmt9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9zd6ty9f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9zd6ty9f/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 65537 65794 - 0 1 chr1 65537 65794 - 0 2 chr1 65537 65794 - 0 3 chr1 65537 65794 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 65537 | 65794 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 65537 65794 - 0 1 chr1 65537 65794 - 0 2 chr1 65537 65794 - 0 3 chr1 65537 65794 - 0 df2 Chromosome Start End Strand Distance 0 chr1 65537 65794 - 0 1 chr1 65537 65794 - 0 2 chr1 65537 65794 - 0 3 chr1 65537 65794 - 0 Actual Chromosome Start End Strand Distance 0 chr1 65537 65794 - 0 1 chr1 65537 65794 - 0 2 chr1 65537 65794 - 0 3 chr1 65537 65794 - 0 Expected Chromosome Start End Strand Distance 0 chr1 65537 65794 - 0 1 chr1 65537 65794 - 0 2 chr1 65537 65794 - 0 3 chr1 65537 65794 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpaarowkrw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaarowkrw/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpoha342nl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoha342nl/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2q12d5m4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2q12d5m4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwzd7hmsd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwzd7hmsd/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpq60nhbsa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq60nhbsa/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptxajxhv8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptxajxhv8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp74v6h_o_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp74v6h_o_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9lbfvzqr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9lbfvzqr/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8a6i6iig/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8a6i6iig/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0c3g_5pw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0c3g_5pw/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpz09j2m4p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz09j2m4p/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpg6nqvysq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg6nqvysq/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7jrocqm3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7jrocqm3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprhrb9ufg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprhrb9ufg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzsr7c471/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzsr7c471/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpit7frpic/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpit7frpic/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpb8msayfl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb8msayfl/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpku1vnva0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpku1vnva0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpo03e9_73/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo03e9_73/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzdf91m5y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzdf91m5y/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdz4_o2gn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdz4_o2gn/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpy8vkfhkf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy8vkfhkf/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpq53vljcn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq53vljcn/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjkwcktt2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjkwcktt2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6cozyf00/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6cozyf00/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp691z4zve/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp691z4zve/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9x613oec/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9x613oec/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0ivvhxu7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0ivvhxu7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptj3y74ja/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptj3y74ja/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyvdtmfak/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyvdtmfak/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9_f60u46/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9_f60u46/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpr3leepta/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr3leepta/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfsw2clz4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfsw2clz4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfb8o_ao1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfb8o_ao1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsyavtthm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsyavtthm/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4li2x3nr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4li2x3nr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpplbif1z5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpplbif1z5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2wroqz6o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2wroqz6o/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmwgsr0na/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmwgsr0na/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe05edz15/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe05edz15/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxyny0otr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxyny0otr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0jnjsjw7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0jnjsjw7/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp85kh5zx8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp85kh5zx8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfop93eli/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfop93eli/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5skjyf1f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5skjyf1f/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpygnassj1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpygnassj1/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpda8i3kne/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpda8i3kne/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5wuusevf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5wuusevf/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqseae6lo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqseae6lo/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2t3ztchc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2t3ztchc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyymo_2bt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyymo_2bt/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptrzxl9j8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptrzxl9j8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpy_pf34bu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy_pf34bu/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuww05yc8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuww05yc8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsvnv8ndo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsvnv8ndo/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdj1wb4a_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdj1wb4a_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmph1t4al3v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph1t4al3v/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpy3ccpo70/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy3ccpo70/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfq2d7mo7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfq2d7mo7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpb3l13zga/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb3l13zga/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpow20y409/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpow20y409/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmkvxcr9v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmkvxcr9v/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpw6cfu5pi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw6cfu5pi/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpp191q2aj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp191q2aj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjb2bcvrw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjb2bcvrw/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptvddkuah/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptvddkuah/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 3 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 3 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 3 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 3 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 3 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3izuj3x8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3izuj3x8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpp1119nf7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp1119nf7/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptah7i64o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptah7i64o/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphldsjxdk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphldsjxdk/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6w5if_qv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6w5if_qv/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5wi2_e51/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5wi2_e51/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________________ test_k_nearest[downstream-True-False-last] __________________ [gw3] linux -- Python 3.12.6 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 880, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 510, in test_k_nearest | @pytest.mark.explore | ^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1722, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 548, in test_k_nearest | result = gr.k_nearest( | ^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2450, in k_nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 292, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 180, in _nearest | df = __nearest(d1, d2, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 115, in nearest_previous | lidx, ridx, dist = nearest_previous_idx(d1, d2, d1.__k__.values, ties) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 28, in nearest_previous_idx | lidx, ridx_pos, dist = k_nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/k_nearest.pyx", line 28, in sorted_nearest.src.k_nearest.k_nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_k_nearest( | nearest_how='downstream', | overlap=True, | strandedness=False, | ties='last', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:14 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:15 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:160 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:171 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:19 | (and 37 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2TAAIyMmGIMAAB5AAQ=') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 548, in test_k_nearest | result = gr.k_nearest( | ^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2450, in k_nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 292, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 180, in _nearest | df = __nearest(d1, d2, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 140, in nearest_next | lidx, ridx, dist = nearest_next_idx(d1, d2, d1.__k__.values, ties) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 56, in nearest_next_idx | lidx, ridx_pos, dist = k_nearest_next_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/k_nearest.pyx", line 55, in sorted_nearest.src.k_nearest.k_nearest_next_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_k_nearest( | nearest_how='downstream', | overlap=True, | strandedness=False, | ties='last', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:160 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:171 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:41 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:42 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:46 | (and 38 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2TABIxYxAAAZAAD') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_z545s27/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_z545s27/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9vwz1bhh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9vwz1bhh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqzajmz45/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqzajmz45/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmplly7oydl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplly7oydl/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfsjnmgvu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfsjnmgvu/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7gr2k8y5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7gr2k8y5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpo4too0uo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo4too0uo/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpt71g82d3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt71g82d3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqjiy3489/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqjiy3489/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmprd5isl38/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprd5isl38/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpte9ti7y5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpte9ti7y5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6l7o0yit/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6l7o0yit/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpq79lxmvf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq79lxmvf/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyil1yrhu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyil1yrhu/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmwdw_e24/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmwdw_e24/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0vfgv2fc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0vfgv2fc/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmyy63i2q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmyy63i2q/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpaclaptgw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaclaptgw/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcvma3iq4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcvma3iq4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1uyut7t2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1uyut7t2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_3c7f23p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_3c7f23p/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp41mkdgey/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp41mkdgey/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3t8x39ou/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3t8x39ou/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpc3r5k0rf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc3r5k0rf/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2aplz46_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2aplz46_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpv6ajnhoj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv6ajnhoj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcqlgvz25/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcqlgvz25/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6he1_v1z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6he1_v1z/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_91mb979/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_91mb979/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpv9m88mqd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv9m88mqd/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpg3zpyqkb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg3zpyqkb/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfvu4e8t2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfvu4e8t2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7kf5xbrr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7kf5xbrr/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp28jiuxls/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp28jiuxls/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7rgpmbjc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7rgpmbjc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpi5stn61l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi5stn61l/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqy4q7i2e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqy4q7i2e/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmphcrttzte/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphcrttzte/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpk3m3wfpg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk3m3wfpg/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbjdkcs8o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbjdkcs8o/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpf7tdnyum/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf7tdnyum/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmphurvdww9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphurvdww9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpa0byclqj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa0byclqj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9st_vgju/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9st_vgju/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp21qdrd4j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp21qdrd4j/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpu09vv5s2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu09vv5s2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmper4tr1rh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmper4tr1rh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjj9ee9gw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjj9ee9gw/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmphuk_ufwh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphuk_ufwh/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7i0qhz7w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7i0qhz7w/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgrua2kdv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgrua2kdv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbvwib3b8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbvwib3b8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpno6x_d7t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpno6x_d7t/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp19srejsu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp19srejsu/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp52pweyq3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp52pweyq3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9p740uhq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9p740uhq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2c3md385/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2c3md385/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpstt6hf9c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpstt6hf9c/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpp7kegxhg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp7kegxhg/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1rnrzt4y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1rnrzt4y/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmivp4q52/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmivp4q52/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsiuqhtqs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsiuqhtqs/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7nuqew8b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7nuqew8b/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp24lyn0rg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp24lyn0rg/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_mj9rvm3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_mj9rvm3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpo_x2_lmr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo_x2_lmr/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmps5wiio0e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps5wiio0e/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpt0cqxpts/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt0cqxpts/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmphmlacdec/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphmlacdec/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4mncjlam/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4mncjlam/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpm3gghekv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm3gghekv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpy9i6puzu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy9i6puzu/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjyirlm7a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjyirlm7a/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzg437n59/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzg437n59/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpymq48fzt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpymq48fzt/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmptjjw7w19/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptjjw7w19/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5qlc5am_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5qlc5am_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpm9bcbs7x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm9bcbs7x/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4c_pt70v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4c_pt70v/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzbki65lg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzbki65lg/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpr3c_z1zi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr3c_z1zi/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxxrn5c49/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxxrn5c49/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwj8bv9se/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwj8bv9se/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0rv08v2b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0rv08v2b/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpp_lkvsbl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp_lkvsbl/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6x12_k20/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6x12_k20/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpy86ko60c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy86ko60c/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6g73m8_c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6g73m8_c/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxmr6hqdw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxmr6hqdw/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9995j3ze/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9995j3ze/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpi16ol94x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi16ol94x/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3bbbv3gm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3bbbv3gm/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpl6lkf_0p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl6lkf_0p/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjs8pg2tm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjs8pg2tm/f2.bed) ----------------------------- Captured stderr call ----------------------------- Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. ___________ test_three_in_a_row[strandedness_chain27-method_chain27] ___________ [gw6] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', False), method_chain = ('nearest', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:63: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('nearest', 'join'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:73 E (and 27 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2QAA0Y4wcDIiCQEY8I5AAESAAk=') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain41-method_chain41] ___________ [gw8] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', False), method_chain = ('subtract', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('subtract', 'join'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:30 E (and 19 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') 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'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +6 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 11 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 6 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ________________________ test_nearest[None-False-False] ________________________ [gw1] linux -- Python 3.12.6 /usr/bin/python3.12 nearest_how = None, overlap = False, strandedness = False @pytest.mark.bedtools > @pytest.mark.parametrize("nearest_how,overlap,strandedness", product(nearest_hows, overlaps, strandedness)) tests/test_binary.py:323: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:351: in test_nearest result = gr.nearest( pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:292: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_nearest( E nearest_how=None, E overlap=False, E strandedness=False, E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:101 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E (and 33 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2TABIxYxAAAZAAD') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpesndz7yc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpesndz7yc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvac0vja2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvac0vja2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2i2lm1h5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2i2lm1h5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpk6nwwnuo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk6nwwnuo/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4cnnn3f8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4cnnn3f8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfkgiodn4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfkgiodn4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqsbiya0f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqsbiya0f/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjepxrqms/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjepxrqms/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfrv5qc48/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfrv5qc48/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpejr2accu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpejr2accu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpl8ullq5q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl8ullq5q/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyf4oq9x1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyf4oq9x1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjpbx6fv0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjpbx6fv0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbo2cszih/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbo2cszih/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpp6_mcbwx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp6_mcbwx/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7rx7c903/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7rx7c903/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpw0o826lj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw0o826lj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpa9cq5_jh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa9cq5_jh/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5oj0bc5_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5oj0bc5_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpw0iwq6t0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw0iwq6t0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpu6nt5btz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu6nt5btz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuqx0bus6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuqx0bus6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptp59qjjp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptp59qjjp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpd3qx_muj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd3qx_muj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpewlsxb0h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpewlsxb0h/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3gn2_0do/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3gn2_0do/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5tm3e4ro/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5tm3e4ro/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptlsg8q5e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptlsg8q5e/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyfmncttt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyfmncttt/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpaukb9up4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaukb9up4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphsvz3dd0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphsvz3dd0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3p3hpbfp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3p3hpbfp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5jke2kis/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5jke2kis/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpb45wr5i9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb45wr5i9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsfty5ofi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsfty5ofi/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppyi8bbj_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppyi8bbj_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmf03201d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmf03201d/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbetp5zyt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbetp5zyt/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6msp8ig7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6msp8ig7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4ezrxxyr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4ezrxxyr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpq40q3h5q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq40q3h5q/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpn0zutrve/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn0zutrve/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpt03reejp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt03reejp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxxt25h0b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxxt25h0b/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_nzn8ydy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_nzn8ydy/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9o347ax6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9o347ax6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpb1zezv7q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb1zezv7q/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpotmusqy7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpotmusqy7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfvndt20k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfvndt20k/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpriitiaxz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpriitiaxz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpze_4cu92/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpze_4cu92/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkkxm_knk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkkxm_knk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphkdov4r6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphkdov4r6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpci5qlz6q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpci5qlz6q/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcux8x04_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcux8x04_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpckui0euj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpckui0euj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2ddbagm5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2ddbagm5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5ac_b9in/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5ac_b9in/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnidynl1e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnidynl1e/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4xzd7pje/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4xzd7pje/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmph3gt05pv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph3gt05pv/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmcuprmtg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmcuprmtg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmidz9tgz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmidz9tgz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbswumdmm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbswumdmm/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpivmsga_n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpivmsga_n/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp13eypp4y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp13eypp4y/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7mhsunm7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7mhsunm7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpf2o1f1m2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf2o1f1m2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpa95kbfmh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa95kbfmh/f2.bed) ___________ test_three_in_a_row[strandedness_chain71-method_chain71] ___________ [gw5] linux -- Python 3.12.6 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 880, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1722, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', 'same'), | method_chain=('nearest', 'set_intersect'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 258 | a | 0 | - | | | chr1 | 113 | 370 | a | 0 | - | | | chr14 | 1 | 258 | a | 0 | - | | | chr14 | 1 | 258 | a | 0 | - | | | chr14 | 1 | 258 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 5 rows and 6 columns from 2 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 6531823 | 6531824 | a | 0 | + | | | chr1 | 6531823 | 6532099 | a | 0 | - | | | chr1 | 6531823 | 6538698 | a | 0 | - | | | chr1 | 65537 | 71879 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 4 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=Empty PyRanges, | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | (and 173 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY7Tt9AxnlPAVD2Y0VDm5lzG3i0mC0VvbspWBkYERCBgYeEEEQwGILQ1kACkQnwEqz8zIyMLIyARkQJVDCKC8ECNUFVgPAzNQKYTFANQBIplAJjCzgthGyaveMTIWMQqDTEySOApSC1LNDLYEaAeDmNQtRiiAWA0iWBggVgEAHPkMfg==') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3688, in set_intersect | other_clusters = other.merge(strand=strand) | ^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 347, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', 'same'), | method_chain=('nearest', 'set_intersect'), | gr=Empty PyRanges, | gr2=Empty PyRanges, | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 | /usr/lib/python3/dist-packages/pandas/core/array_algos/take.py:574 | (and 78 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain108-method_chain108] __________ [gw10] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', 'opposite') method_chain = ('set_intersect', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('set_intersect', 'nearest'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 E /usr/lib/python3/dist-packages/pandas/core/array_algos/take.py:574 E (and 61 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BMTDE7EqC8mpGRAQsAAEpkAuE=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') __________ test_three_in_a_row[strandedness_chain123-method_chain123] __________ [gw7] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', 'opposite') method_chain = ('nearest', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('nearest', 'intersect'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 9999999 | 10000000 | a | 0 | - | E | chr1 | 9999999 | 10000000 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:53 E (and 28 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2QAA0YGOGBk5AcRUGEIPWNaHQofCAAh2QHG') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________________ test_nearest[downstream-False-opposite] ____________________ [gw2] linux -- Python 3.12.6 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 880, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 323, in test_nearest | @pytest.mark.parametrize("nearest_how,overlap,strandedness", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1722, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 351, in test_nearest | result = gr.nearest( | ^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 118, in _nearest | r_idx, dist = _previous_nonoverlapping(df_to_find_nearest_in.Start, | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_nearest( | nearest_how='downstream', | overlap=False, | strandedness='opposite', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | | chr1 | 1 | 2 | a | 0 | - | | | chr1 | 1 | 2 | a | 0 | - | | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 4 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | (and 103 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2RgYGBkZACRQMwMIpggbJA4I5gAASYYHwpgTIQIAwMABYUAHg==') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 351, in test_nearest | result = gr.nearest( | ^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 115, in _nearest | r_idx, dist = _next_nonoverlapping(df_to_find_nearest_in.End, | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 62, in _next_nonoverlapping | r_idx, dist = nearest_next_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 34, in sorted_nearest.src.sorted_nearest.nearest_next_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_nearest( | nearest_how='downstream', | overlap=False, | strandedness='opposite', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | | chr1 | 1 | 258 | a | 0 | - | | | chr1 | 1 | 258 | a | 0 | - | | | chr1 | 1 | 258 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 4 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 258 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | (and 103 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2RgYGBkZACR9sF2fxjjXBUygGwGRrA4I1gSgkBciEIGMAALAQCR4gMQ') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvf_ghnt5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvf_ghnt5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp396xqx65/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp396xqx65/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdld6oj0k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdld6oj0k/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5kyip3eo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5kyip3eo/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpirwfz_tu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpirwfz_tu/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvcqb5w83/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvcqb5w83/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpye6vwdlj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpye6vwdlj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpj9rkrfvi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj9rkrfvi/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkf99vbi6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkf99vbi6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppxtqmtr7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppxtqmtr7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxz4sw4lk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxz4sw4lk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpiryif3uu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiryif3uu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqumjl82p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqumjl82p/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgzkstqek/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgzkstqek/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfehnrg3m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfehnrg3m/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpoz3__5ub/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoz3__5ub/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprkno7hvp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprkno7hvp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmps7ga9gha/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps7ga9gha/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnujnvtkj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnujnvtkj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjtpxinq6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjtpxinq6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptq04h4p3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptq04h4p3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptz67_8ks/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptz67_8ks/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmjn8epyh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmjn8epyh/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvw8e0axp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvw8e0axp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpirvqkdc3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpirvqkdc3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpme56h5y1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpme56h5y1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfslscjvo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfslscjvo/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpr82wpw0n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr82wpw0n/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp55iel8kc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp55iel8kc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8k3b0law/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8k3b0law/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_dr1b8qd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_dr1b8qd/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpm4kwblbd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm4kwblbd/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpg7grwuay/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg7grwuay/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphx9php69/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphx9php69/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8hzpq3kh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8hzpq3kh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpv18_bgbe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv18_bgbe/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplcconbih/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplcconbih/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2lr5stql/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2lr5stql/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2sgwg76b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2sgwg76b/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwlxr23bq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwlxr23bq/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpih71i2oh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpih71i2oh/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuxdz8e5h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuxdz8e5h/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdd8nnwkh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdd8nnwkh/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpq4g9oetg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq4g9oetg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprtq8u7k7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprtq8u7k7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpau1im3d9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpau1im3d9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8te28cix/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8te28cix/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkm1yh16w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkm1yh16w/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5kv22vai/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5kv22vai/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfwzj1whq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfwzj1whq/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpb3egtd57/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb3egtd57/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphtlw8fls/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphtlw8fls/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp51z1v8ka/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp51z1v8ka/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkdpao9by/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkdpao9by/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprn6ajqgj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprn6ajqgj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjocc7d69/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjocc7d69/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpncc6b4_n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpncc6b4_n/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmxkp9ba3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmxkp9ba3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfprape9c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfprape9c/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmmozm51j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmmozm51j/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpa42i1by0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa42i1by0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5yk00ooj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5yk00ooj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0w3thtoq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0w3thtoq/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnp606uie/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnp606uie/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9qo_p4fx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9qo_p4fx/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7iajka43/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7iajka43/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxfnydddh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxfnydddh/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuqlx0u4r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuqlx0u4r/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpunesg53v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpunesg53v/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjp__707u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjp__707u/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppz9gr06g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppz9gr06g/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4yxk7dss/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4yxk7dss/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2gmm09p_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2gmm09p_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpl0plr7b2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl0plr7b2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpy1afwqza/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy1afwqza/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpp9qlm6i1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp9qlm6i1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplf1y3o_u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplf1y3o_u/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5hxg0wlz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5hxg0wlz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpiibthiox/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiibthiox/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpz6rzbxtq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz6rzbxtq/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptide3ufx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptide3ufx/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7jyer3_a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7jyer3_a/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpi148m0ku/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi148m0ku/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdnm0nsrp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdnm0nsrp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp44zoep_n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp44zoep_n/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe28tsc8s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe28tsc8s/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkt5izhhy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkt5izhhy/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplr82gd1k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplr82gd1k/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprl364ws5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprl364ws5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmph8pydnrf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph8pydnrf/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp230r16jz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp230r16jz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0y6oxtzw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0y6oxtzw/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8dxgxp6_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8dxgxp6_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpofne4o7l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpofne4o7l/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvne39gcc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvne39gcc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpubra2sb_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpubra2sb_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpn0_m_eft/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn0_m_eft/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0tfsgwlu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0tfsgwlu/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpb852hm9m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb852hm9m/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5113t20w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5113t20w/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp349n0g61/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp349n0g61/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjx26vvcy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjx26vvcy/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbasvq3o5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbasvq3o5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpja5eq6bc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpja5eq6bc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp809o8a1l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp809o8a1l/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8pij7h1z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8pij7h1z/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptdbbqurs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptdbbqurs/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpctbdbl4_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpctbdbl4_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpa7werhz7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa7werhz7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpi64q4vz9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi64q4vz9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpo26zy8cs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo26zy8cs/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7msq18vh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7msq18vh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpc6wn54de/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc6wn54de/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3e2jspfc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3e2jspfc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphrf5zyyg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphrf5zyyg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwj0off4j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwj0off4j/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpw632kjej/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw632kjej/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgpqycqm2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgpqycqm2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpeubdr2ma/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpeubdr2ma/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4yjc7wsu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4yjc7wsu/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpptmlhz_b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpptmlhz_b/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpj5x77h8k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj5x77h8k/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpw5mptjhk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw5mptjhk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpobpstf7c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpobpstf7c/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjd0bhez_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjd0bhez_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvwjt7fgt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvwjt7fgt/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1yd1mx4e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1yd1mx4e/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvbkc0bzc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvbkc0bzc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptt_i3blw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptt_i3blw/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0hk0_vk5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0hk0_vk5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp56b1j9uu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp56b1j9uu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9up3nffv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9up3nffv/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4iqa0rbb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4iqa0rbb/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6w6edq5m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6w6edq5m/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2rfnpbj8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2rfnpbj8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8s6rv6gb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8s6rv6gb/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmhnv4dur/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmhnv4dur/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpljbthfj6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpljbthfj6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpoc77ptmi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoc77ptmi/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcyhiw7t2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcyhiw7t2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp64k8vlp6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp64k8vlp6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpc1os2lv6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc1os2lv6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp70nvg5u8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp70nvg5u8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpq3rs9br9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq3rs9br9/f2.bed) ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ________________________ test_nearest[None-False-same] _________________________ [gw1] linux -- Python 3.12.6 /usr/bin/python3.12 nearest_how = None, overlap = False, strandedness = 'same' @pytest.mark.bedtools > @pytest.mark.parametrize("nearest_how,overlap,strandedness", product(nearest_hows, overlaps, strandedness)) tests/test_binary.py:323: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:351: in test_nearest result = gr.nearest( pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_nearest( E nearest_how=None, E overlap=False, E strandedness='same', E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 E (and 105 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2TABIxYxAAAZAAD') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpc6813kiu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc6813kiu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdm_txx8v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdm_txx8v/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpy6eequ5g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy6eequ5g/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3zu87sss/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3zu87sss/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpl70f9wd0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl70f9wd0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplv8z83uy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplv8z83uy/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpev07907a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpev07907a/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp25qdja_n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp25qdja_n/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpndkgjb6v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpndkgjb6v/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp968nxysk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp968nxysk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmputzx3wdj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmputzx3wdj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmph3cgc4oi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph3cgc4oi/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgmminx9x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgmminx9x/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprhd3m6tz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprhd3m6tz/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp15y3fqic/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp15y3fqic/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcbabcl77/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcbabcl77/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqttr1nel/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqttr1nel/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplgl2qvnc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplgl2qvnc/f2.bed) ___________ test_three_in_a_row[strandedness_chain94-method_chain94] ___________ [gw9] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', 'same'), method_chain = ('join', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:68: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2, suffix="_c") pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('join', 'nearest'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | - | E | chr1 | 1 | 2 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 3 | a | 0 | - | E | chr1 | 1 | 2 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 4 | 261 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:53 E (and 28 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY0xVyJ/GWNy2TIKBkZGRgZEBDEAUIyMzA0M1oyxUACIEYzMyRsHZDMwMwkCSEQAIPwRk') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1952831 | 1954851 | a | 0 | ... | | chr1 | 761558 | 763578 | a | 0 | ... | | chr1 | 6787928 | 6797928 | a | 0 | ... | | chr20 | 3083917 | 3085937 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 17 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain84-method_chain84] ___________ [gw4] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', 'same'), method_chain = ('subtract', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('subtract', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:112 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:117 E (and 130 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2CUUlQ5ZSWkxcjAyIAJACplAaM=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. _________________ test_k_nearest[upstream-False-opposite-last] _________________ [gw3] linux -- Python 3.12.6 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 880, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 510, in test_k_nearest | @pytest.mark.explore | ^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1722, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 548, in test_k_nearest | result = gr.k_nearest( | ^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2450, in k_nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 180, in _nearest | df = __nearest(d1, d2, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 140, in nearest_next | lidx, ridx, dist = nearest_next_idx(d1, d2, d1.__k__.values, ties) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 56, in nearest_next_idx | lidx, ridx_pos, dist = k_nearest_next_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/k_nearest.pyx", line 55, in sorted_nearest.src.k_nearest.k_nearest_next_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_k_nearest( | nearest_how='upstream', | overlap=False, | strandedness='opposite', | ties='last', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 7095 | a | 0 | - | | | chr18 | 1 | 7095 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr18 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:160 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:171 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:41 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:42 | (and 41 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2TIFfzNaKrDk8XAyMggyMDIwMUABDnSW4F8sDADWBQIwBIAlNgEog==') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 548, in test_k_nearest | result = gr.k_nearest( | ^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2450, in k_nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 180, in _nearest | df = __nearest(d1, d2, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 115, in nearest_previous | lidx, ridx, dist = nearest_previous_idx(d1, d2, d1.__k__.values, ties) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py", line 28, in nearest_previous_idx | lidx, ridx_pos, dist = k_nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/k_nearest.pyx", line 28, in sorted_nearest.src.k_nearest.k_nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_k_nearest( | nearest_how='upstream', | overlap=False, | strandedness='opposite', | ties='last', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:14 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:15 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:160 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:171 | (and 40 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2TABIwoFJgJAABuAAU=') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdt7xec56/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdt7xec56/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpy0ere9hn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy0ere9hn/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpg20e973v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg20e973v/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp00g_j5w9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp00g_j5w9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpa70ryoa8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa70ryoa8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5kmh7ne_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5kmh7ne_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp59fs6pfj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp59fs6pfj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwf24_ezn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwf24_ezn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpukr71_il/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpukr71_il/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0u61as06/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0u61as06/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdbvt2ns9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdbvt2ns9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8l3e1okr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8l3e1okr/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmptj6joozp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptj6joozp/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp57ttb4xw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp57ttb4xw/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvxvqfuqq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvxvqfuqq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjnds9uvf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjnds9uvf/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdmu96anm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdmu96anm/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbx0xchf0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbx0xchf0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpj5os_w0h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj5os_w0h/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5z_36m6p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5z_36m6p/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyfmb1ji8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyfmb1ji8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp387cfo_h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp387cfo_h/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpj94gvo22/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj94gvo22/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_g48u6f0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_g48u6f0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8pmpd1lb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8pmpd1lb/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpynzb9q2p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpynzb9q2p/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkudkt90y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkudkt90y/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7l1uncc0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7l1uncc0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3cylcc4n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3cylcc4n/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp754m7eh0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp754m7eh0/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpci_1hk89/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpci_1hk89/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpajfzvsb9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpajfzvsb9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5ry51pxx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5ry51pxx/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpi0xercl5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi0xercl5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnnk9r80u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnnk9r80u/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2uo0ula2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2uo0ula2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpoz16t8ac/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoz16t8ac/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgzgnriqo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgzgnriqo/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmphynf6jqf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphynf6jqf/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmplu2_fwoe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplu2_fwoe/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3igtubop/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3igtubop/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkf8cl_ik/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkf8cl_ik/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpv184aqyd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv184aqyd/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpd_08_d1e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd_08_d1e/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmm1fkk08/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmm1fkk08/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1esu20z7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1esu20z7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp924nsbbn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp924nsbbn/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwudrl1e5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwudrl1e5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmplynozade/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplynozade/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8iedb1f_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8iedb1f_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjemw19vo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjemw19vo/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7jop_12j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7jop_12j/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpka0ohgtd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpka0ohgtd/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpn0nm2vax/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn0nm2vax/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpk5dumtnr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk5dumtnr/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5oqv_lgz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5oqv_lgz/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6cin6w_z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6cin6w_z/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp47a5l_k0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp47a5l_k0/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8321ltjr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8321ltjr/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpazokw9sp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpazokw9sp/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpixp_ue8l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpixp_ue8l/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpb4ji_1d8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb4ji_1d8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpaxuq10xm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaxuq10xm/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyr0boou9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyr0boou9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpm8ku8c55/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm8ku8c55/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpj_ujmwds/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj_ujmwds/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpex4syhy3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpex4syhy3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpf_rjedpi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf_rjedpi/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpv9ch_h57/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv9ch_h57/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0va97qvj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0va97qvj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0il_qxfg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0il_qxfg/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_18kerwk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_18kerwk/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_o2xn3_k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_o2xn3_k/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcr7xxt5h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcr7xxt5h/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpm3ia3krv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm3ia3krv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbdgf_4r5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbdgf_4r5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpp_osqz0b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp_osqz0b/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp06rso1w2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp06rso1w2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0xseay0a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0xseay0a/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9mclh7oe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9mclh7oe/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3631dv6k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3631dv6k/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgf_q9rcw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgf_q9rcw/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp014htmvx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp014htmvx/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkc9bxx41/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkc9bxx41/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_z1gtqml/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_z1gtqml/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfqvdwcmv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfqvdwcmv/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9xqm58h8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9xqm58h8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2dbl8a73/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2dbl8a73/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvdo_4psr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvdo_4psr/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3fgziq9g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3fgziq9g/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmppnhlsn3x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppnhlsn3x/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmplojng0jx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplojng0jx/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjgm_ojz3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjgm_ojz3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbebifs1i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbebifs1i/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpe4fnqr2d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe4fnqr2d/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfuw2b3oz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfuw2b3oz/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3a4uvxjt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3a4uvxjt/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwdt8s9zd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwdt8s9zd/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_ge4toae/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_ge4toae/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcorwnl3v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcorwnl3v/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpr721y_eg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr721y_eg/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpf6jsyq93/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf6jsyq93/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0se8krv3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0se8krv3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbrpfe_57/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbrpfe_57/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpclknjp6_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpclknjp6_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4k_4_xdm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4k_4_xdm/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyl6iikq7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyl6iikq7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp60p6yp_0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp60p6yp_0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpewdpc7u3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpewdpc7u3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmgrg967y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmgrg967y/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpk7dhz8zj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk7dhz8zj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsybth5j1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsybth5j1/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_etcbv8w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_etcbv8w/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_njnewji/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_njnewji/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpccrp2vq7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpccrp2vq7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpito27rt3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpito27rt3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmdkoh05p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmdkoh05p/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqe4fi8fl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqe4fi8fl/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpo6lo9u7d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo6lo9u7d/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpilfgczjv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpilfgczjv/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpaqnl99jk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaqnl99jk/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2alz679c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2alz679c/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpx7c7fp2i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx7c7fp2i/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5nfsnk7k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5nfsnk7k/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqckqlo8c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqckqlo8c/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdp16mc1l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdp16mc1l/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpouanx368/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpouanx368/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4p2pshxp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4p2pshxp/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmphnpd8j7s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphnpd8j7s/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjfyi2qp7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjfyi2qp7/f2.bed) ----------------------------- Captured stderr call ----------------------------- Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr11 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr11 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr11 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr11 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr11 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr11 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr18 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr18 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr11 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr18 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr18 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr18 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr18 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr18 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr18 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr18 than requested (2). It is likely that there are fewer total records on that chromosome than requested. ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ______________________ test_nearest[None-False-opposite] _______________________ [gw1] linux -- Python 3.12.6 /usr/bin/python3.12 nearest_how = None, overlap = False, strandedness = 'opposite' @pytest.mark.bedtools > @pytest.mark.parametrize("nearest_how,overlap,strandedness", product(nearest_hows, overlaps, strandedness)) tests/test_binary.py:323: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:351: in test_nearest result = gr.nearest( pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_nearest( E nearest_how=None, E overlap=False, E strandedness='opposite', E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 E (and 101 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2TABIwoFJgJAABuAAU=') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkdpd21x_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkdpd21x_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe4bjr2bo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe4bjr2bo/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp17wewuyx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp17wewuyx/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppfn4ti3q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppfn4ti3q/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp06_ndpxo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp06_ndpxo/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpus5cryme/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpus5cryme/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpr50dktsb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr50dktsb/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2go_3430/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2go_3430/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpc_tp_vfm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc_tp_vfm/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpey36ocfs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpey36ocfs/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplbukicsu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplbukicsu/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2ywqhnnx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2ywqhnnx/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprfqn8v2h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprfqn8v2h/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphmk73q5_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphmk73q5_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpz9rd4jvx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz9rd4jvx/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbkte7cq2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbkte7cq2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmyvn0y__/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmyvn0y__/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmps_98203e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps_98203e/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6yzc6h6t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6yzc6h6t/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptam_n4ub/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptam_n4ub/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyn2njrh4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyn2njrh4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3e47rtm2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3e47rtm2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmgd6n4xv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmgd6n4xv/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpz1925lpu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz1925lpu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1_dig23u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1_dig23u/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp06awk454/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp06awk454/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6uz8zq4r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6uz8zq4r/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdp5ez3ty/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdp5ez3ty/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_374_b5c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_374_b5c/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5qmjim36/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5qmjim36/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_n9g54dk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_n9g54dk/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpktgtxeyd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpktgtxeyd/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbo651pj0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbo651pj0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjljyam06/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjljyam06/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpb8m3fm69/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb8m3fm69/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2mcqyh79/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2mcqyh79/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprlayctsi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprlayctsi/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2mrs33ip/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2mrs33ip/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1ius_dvf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1ius_dvf/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpa96l0lrg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa96l0lrg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpn3gb9n46/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn3gb9n46/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptb8meuq2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptb8meuq2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkbt82t5s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkbt82t5s/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1f4v5r3d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1f4v5r3d/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp36_be4u4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp36_be4u4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe6d5bjk5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe6d5bjk5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9n_50we2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9n_50we2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmyhfer7e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmyhfer7e/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp40myd39z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp40myd39z/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpejoz0k0r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpejoz0k0r/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfgdb4es0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfgdb4es0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbsqewunt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbsqewunt/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2hoeu04b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2hoeu04b/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe7v76or3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe7v76or3/f2.bed) ___________ test_three_in_a_row[strandedness_chain28-method_chain28] ___________ [gw6] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', False), method_chain = ('intersect', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('intersect', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:33 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:41 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:17 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:21 E (and 144 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain109-method_chain109] __________ [gw10] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', 'opposite') method_chain = ('set_intersect', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('set_intersect', 'intersect'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E (and 65 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2CAA0YGLAAAADUAAg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ___________ test_three_in_a_row[strandedness_chain42-method_chain42] ___________ [gw8] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', False), method_chain = ('join', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('join', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:33 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:41 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:17 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:21 E (and 96 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. _____________________________ test_jaccard[False] ______________________________ [gw2] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness = False @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness", no_opposite) tests/test_binary.py:363: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:378: in test_jaccard result = gr.stats.jaccard(gr2, strandedness=strandedness) pyranges/statistics.py:766: in jaccard for v in self.set_intersect(other).lengths(as_dict=True).values()) pyranges/pyranges.py:3687: in set_intersect self_clusters = self.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_jaccard( E strandedness=False, E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., # or any other generated value E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2TABIxYxAAAZAAD') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain72-method_chain72] ___________ [gw5] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', 'same'), method_chain = ('nearest', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('nearest', 'overlap'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | - | E | chr1 | 2 | 3 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:53 E (and 28 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2QAA0YGOGBkhAkwAtlAwMCIUIGkjgEAAfkADw==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 14 | 271 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain124-method_chain124] __________ [gw7] linux -- Python 3.12.6 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 880, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1722, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', 'opposite'), | method_chain=('nearest', 'subtract'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 65537 | 65540 | a | 0 | - | | | chr1 | 65537 | 65538 | a | 0 | - | | | chr1 | 4 | 7 | a | 0 | - | | | chr1 | 4 | 5 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 4 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | | chr1 | 2 | 3 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 258 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | (and 173 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicYxSd0reEkcnbtIfRWGzjUkYrhdd2DIyMjBDMwABiMIAoBmZGZhAfymUCq2CEkowQGRApDSIgKiH6YCwoE6ELLAYWhVnEyAhTBoVgpgwjxBwA9TcGnA==') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 4384, in subtract | other_clusters = other.merge(strand=strand) | ^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 347, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', 'opposite'), | method_chain=('nearest', 'subtract'), | gr=Empty PyRanges, | gr2=Empty PyRanges, # or any other generated value | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 | /usr/lib/python3/dist-packages/pandas/core/array_algos/take.py:574 | (and 84 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain96-method_chain96] ___________ [gw9] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', 'same'), method_chain = ('join', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('join', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:145 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 E (and 19 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ___________ test_three_in_a_row[strandedness_chain85-method_chain85] ___________ [gw4] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', 'same') method_chain = ('subtract', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('subtract', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:112 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:117 E (and 119 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2D0UL992owni5GBkQETAABIdgLF') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ______________________ test_nearest[upstream-True-False] _______________________ [gw1] linux -- Python 3.12.6 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 880, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 323, in test_nearest | @pytest.mark.parametrize("nearest_how,overlap,strandedness", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1722, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 3 distinct failures. (3 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 351, in test_nearest | result = gr.nearest( | ^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 292, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 115, in _nearest | r_idx, dist = _next_nonoverlapping(df_to_find_nearest_in.End, | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 62, in _next_nonoverlapping | r_idx, dist = nearest_next_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 34, in sorted_nearest.src.sorted_nearest.nearest_next_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_nearest( | nearest_how='upstream', | overlap=True, | strandedness=False, | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:11 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:12 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:101 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 | (and 65 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2TAAIyMKDwIBQAAgAAF') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 351, in test_nearest | result = gr.nearest( | ^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 292, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 118, in _nearest | r_idx, dist = _previous_nonoverlapping(df_to_find_nearest_in.Start, | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_nearest( | nearest_how='upstream', | overlap=True, | strandedness=False, | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:11 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:12 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:101 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 | (and 68 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2TABIxYOAAAawAE') as a decorator on your test case +---------------- 3 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 359, in test_nearest | compare_results_nearest(bedtools_df, result) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py", line 107, in compare_results_nearest | assert_df_equal(result_df, bedtools_df) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/helpers.py", line 60, in assert_df_equal | pd.testing.assert_frame_equal(df1, df2) | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 1279, in assert_frame_equal | assert_series_equal( | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 975, in assert_series_equal | assert_attr_equal("dtype", left, right, obj=f"Attributes of {obj}") | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 421, in assert_attr_equal | raise_assert_detail(obj, msg, left_attr, right_attr) | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 614, in raise_assert_detail | raise AssertionError(msg) | AssertionError: Attributes of DataFrame.iloc[:, 4] (column name="Distance") are different | | Attribute "dtype" are different | [left]: int32 | [right]: int64 | Falsifying example: test_nearest( | nearest_how='upstream', | overlap=True, | strandedness=False, | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/init.py:174 | (and 449 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2TABIxYxAAAZAAD') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp93c3bpnp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp93c3bpnp/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpaldcrs82/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaldcrs82/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpspamfg8z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpspamfg8z/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0naisnw7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0naisnw7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpo6zkkk2t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo6zkkk2t/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 3 4 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 2 chr1 1 2 - 0 1 chr1 3 4 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 3 4 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 3 4 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 3 4 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpt9hhd5vt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt9hhd5vt/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 3 4 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 2 chr1 1 2 - 0 1 chr1 3 4 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 3 4 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 3 4 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 3 4 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzfmpj8zh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzfmpj8zh/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 3 4 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 2 chr1 1 2 - 0 1 chr1 3 4 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 3 4 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 3 4 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 3 4 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpg4zkv00h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg4zkv00h/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 3 4 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 2 chr1 1 2 - 0 1 chr1 3 4 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 3 4 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 3 4 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 3 4 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpy3gistr9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy3gistr9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjkfbj7um/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjkfbj7um/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5emwr4f9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5emwr4f9/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfjslqjln/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfjslqjln/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpg8cam39g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg8cam39g/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1y5sdbu0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1y5sdbu0/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpenr8yias/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpenr8yias/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgawbff50/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgawbff50/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpee3y3ie7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpee3y3ie7/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyfyk61ua/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyfyk61ua/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1dwxtv59/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1dwxtv59/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpu_xcf5wh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu_xcf5wh/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppus10x5v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppus10x5v/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2n_hdxlw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2n_hdxlw/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5u9v9svj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5u9v9svj/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0ub4knq6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0ub4knq6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3pnsglx5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3pnsglx5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpk7t3fj7g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk7t3fj7g/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpo79zohc3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo79zohc3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp19nkjn28/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp19nkjn28/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqf34u0b_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqf34u0b_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplb423czf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplb423czf/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5_jd_tdc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5_jd_tdc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe5gt61em/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe5gt61em/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4xap4bi7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4xap4bi7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpclh5_2au/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpclh5_2au/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpboj3jzx6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpboj3jzx6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpax4gm7ah/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpax4gm7ah/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfku4mk6d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfku4mk6d/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5yqn_7xp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5yqn_7xp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmph2o58fh7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph2o58fh7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7_8z66tu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7_8z66tu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp70wqayyw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp70wqayyw/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprl7a4dhc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprl7a4dhc/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpoc6xhrgr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoc6xhrgr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxc2g409u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxc2g409u/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpowctqgsp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpowctqgsp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzhvazgr8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzhvazgr8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4azehib6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4azehib6/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnsc4dccn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnsc4dccn/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpq7axajpi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq7axajpi/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5pc7sql7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5pc7sql7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppuzm3nmn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppuzm3nmn/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpt9y4uns_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt9y4uns_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptdeyt44v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptdeyt44v/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdc0sus1a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdc0sus1a/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpt8i3xlsy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt8i3xlsy/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpg9u3d9j0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg9u3d9j0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbu5n0fi4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbu5n0fi4/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgeqo0v9r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgeqo0v9r/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgfbhtf7m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgfbhtf7m/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprgf8oaj3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprgf8oaj3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpj5q3xts7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj5q3xts7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvgsaqzdu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvgsaqzdu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpw4qjccon/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw4qjccon/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqc2je36b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqc2je36b/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgtexrw5k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgtexrw5k/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 + 0 1 chr1 2 3 + 0 2 chr1 2 3 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 2 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 + 0 1 chr1 2 3 + 0 2 chr1 2 3 + 0 df2 Chromosome Start End Strand Distance 0 chr1 2 3 + 0 1 chr1 2 3 + 0 2 chr1 2 3 + 0 Actual Chromosome Start End Strand Distance 0 chr1 2 3 + 0 1 chr1 2 3 + 0 2 chr1 2 3 + 0 Expected Chromosome Start End Strand Distance 0 chr1 2 3 + 0 1 chr1 2 3 + 0 2 chr1 2 3 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_j_c2l_p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_j_c2l_p/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 + 0 1 chr1 2 3 + 0 2 chr1 2 3 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 2 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 + 0 1 chr1 2 3 + 0 2 chr1 2 3 + 0 df2 Chromosome Start End Strand Distance 0 chr1 2 3 + 0 1 chr1 2 3 + 0 2 chr1 2 3 + 0 Actual Chromosome Start End Strand Distance 0 chr1 2 3 + 0 1 chr1 2 3 + 0 2 chr1 2 3 + 0 Expected Chromosome Start End Strand Distance 0 chr1 2 3 + 0 1 chr1 2 3 + 0 2 chr1 2 3 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvesva3ti/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvesva3ti/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzw9iynp8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzw9iynp8/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 258 + 0 1 chr1 1 258 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 258 | a | 0 | ... | | chr1 | 1 | 258 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 258 + 0 1 chr1 1 258 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 258 + 0 1 chr1 1 258 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 258 + 0 1 chr1 1 258 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 258 + 0 1 chr1 1 258 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7xr8eeqw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7xr8eeqw/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5c2rdmcb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5c2rdmcb/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 + 0 1 chr1 2 3 + 0 2 chr1 2 3 + 0 3 chr1 2 3 + 0 4 chr1 2 3 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 2 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 + 0 1 chr1 2 3 + 0 2 chr1 2 3 + 0 3 chr1 2 3 + 0 4 chr1 2 3 + 0 df2 Chromosome Start End Strand Distance 0 chr1 2 3 + 0 1 chr1 2 3 + 0 2 chr1 2 3 + 0 3 chr1 2 3 + 0 4 chr1 2 3 + 0 Actual Chromosome Start End Strand Distance 0 chr1 2 3 + 0 1 chr1 2 3 + 0 2 chr1 2 3 + 0 3 chr1 2 3 + 0 4 chr1 2 3 + 0 Expected Chromosome Start End Strand Distance 0 chr1 2 3 + 0 1 chr1 2 3 + 0 2 chr1 2 3 + 0 3 chr1 2 3 + 0 4 chr1 2 3 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmporbe4q8t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmporbe4q8t/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzbh0q5e1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzbh0q5e1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7ntmgo35/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7ntmgo35/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpc3e4ptaq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc3e4ptaq/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpeg4cd09n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpeg4cd09n/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7y41vurh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7y41vurh/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 + 0 1 chr1 2 3 + 0 2 chr1 2 3 + 0 3 chr1 2 3 + 0 4 chr1 2 3 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 2 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 + 0 1 chr1 2 3 + 0 2 chr1 2 3 + 0 3 chr1 2 3 + 0 4 chr1 2 3 + 0 df2 Chromosome Start End Strand Distance 0 chr1 2 3 + 0 1 chr1 2 3 + 0 2 chr1 2 3 + 0 3 chr1 2 3 + 0 4 chr1 2 3 + 0 Actual Chromosome Start End Strand Distance 0 chr1 2 3 + 0 1 chr1 2 3 + 0 2 chr1 2 3 + 0 3 chr1 2 3 + 0 4 chr1 2 3 + 0 Expected Chromosome Start End Strand Distance 0 chr1 2 3 + 0 1 chr1 2 3 + 0 2 chr1 2 3 + 0 3 chr1 2 3 + 0 4 chr1 2 3 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp823j1psr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp823j1psr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpku5a6ck5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpku5a6ck5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcadq0v6y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcadq0v6y/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmporsig1nm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmporsig1nm/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpph6roh0u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpph6roh0u/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8804mok_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8804mok_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcner128y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcner128y/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpoyw02f2d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoyw02f2d/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpx3pul15o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx3pul15o/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsiykjajz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsiykjajz/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_kohf7aq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_kohf7aq/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmper28m626/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmper28m626/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpez0z1fzk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpez0z1fzk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzzk_kc2_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzzk_kc2_/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5d3e5q8w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5d3e5q8w/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4buu03j3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4buu03j3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0us031hi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0us031hi/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp11fnwdcy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp11fnwdcy/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpp43wzypf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp43wzypf/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfkn20ub_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfkn20ub_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkfm1qdd_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkfm1qdd_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpold6r5rw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpold6r5rw/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdql3k1v8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdql3k1v8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5lzh09k_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5lzh09k_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpccgvjrzu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpccgvjrzu/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvehsocnb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvehsocnb/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3118evc5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3118evc5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpoacnsg09/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoacnsg09/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] __________ test_three_in_a_row[strandedness_chain137-method_chain137] __________ [gw3] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', 'opposite') method_chain = ('subtract', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('subtract', 'intersect'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:30 E /usr/lib/python3/dist-packages/pandas/core/dtypes/missing.py:207 E (and 18 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') __________ test_three_in_a_row[strandedness_chain150-method_chain150] __________ [gw8] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', False) method_chain = ('set_union', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('set_union', 'nearest'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E (and 197 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2DUTAztsxY6wsDIgAUAAEAFAoE=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ___________ test_three_in_a_row[strandedness_chain29-method_chain29] ___________ [gw6] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', False) method_chain = ('intersect', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('intersect', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:15 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:145 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:369 E (and 23 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BAAEYUCgwAAD4AAw==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') __________ test_three_in_a_row[strandedness_chain110-method_chain110] __________ [gw10] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', 'opposite') method_chain = ('set_intersect', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('set_intersect', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E (and 103 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2Bk94k8xKO4hpGBkQETAAA6UQJL') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain73-method_chain73] ___________ [gw5] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', 'same'), method_chain = ('nearest', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:63: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('nearest', 'nearest'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:53 E (and 29 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2QAA0YGOGBEYsMkGBEKAADuAAg=') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +13 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4095239 | 4095247 | a | 0 | ... | | chr1 | 1 | 4279 | a | 0 | ... | | chr1 | 4095239 | 4095240 | a | 0 | ... | | chr1 | 4095239 | 4095246 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 18 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 13 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance, ... (+ 6 more.) ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +13 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 65543 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 18 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 13 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance, ... (+ 6 more.) ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain151-method_chain151] __________ [gw8] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', False) method_chain = ('set_union', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('set_union', 'intersect'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E (and 196 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2CAA0YGLAAAADUAAg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') __________ test_three_in_a_row[strandedness_chain138-method_chain138] __________ [gw3] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', 'opposite') method_chain = ('subtract', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('subtract', 'subtract'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:30 E (and 19 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 65537 | 65538 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') __________ test_three_in_a_row[strandedness_chain125-method_chain125] __________ [gw7] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', 'opposite'), method_chain = ('nearest', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:63: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('nearest', 'join'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:73 E (and 27 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2RAAozYKChH0dynSYtblwEACMABjg==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain86-method_chain86] ___________ [gw4] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', 'same'), method_chain = ('subtract', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('subtract', 'overlap'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:30 E /usr/lib/python3/dist-packages/pandas/core/dtypes/missing.py:207 E (and 18 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') __________ test_three_in_a_row[strandedness_chain164-method_chain164] __________ [gw2] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', False), method_chain = ('overlap', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:292: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('overlap', 'nearest'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 7 | 1154 | a | 0 | + | E | chr1 | 7 | 1154 | a | 0 | + | E | chr1 | 7 | 1154 | a | 0 | + | E | chr1 | 7 | 1154 | a | 0 | + | E | chr1 | 7 | 1154 | a | 0 | + | E | chr1 | 7 | 1154 | a | 0 | - | E | chr1 | 7 | 1154 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 7 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E | chr1 | 1 | 9 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:53 E (and 29 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY+Q2XJnEKGtyKJRRT9hGlzHY60U9Y6qVxQZGBgYGRhABohgZmRgZQJCBjcGCpYoRLMXIxMDIApJjZWBkY2BkZWQGq4DpYoDyQCQYsYNpiAwCAABmRgfq') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain175-method_chain175] __________ [gw1] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', False) method_chain = ('intersect', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('intersect', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:33 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E (and 218 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ___________ test_three_in_a_row[strandedness_chain98-method_chain98] ___________ [gw9] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', 'opposite') method_chain = ('set_union', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('set_union', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E (and 250 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2CUsyx+4CvvwsjAyIAJAD1zAl4=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain111-method_chain111] __________ [gw10] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', 'opposite') method_chain = ('set_intersect', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('set_intersect', 'join'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 E /usr/lib/python3/dist-packages/pandas/core/array_algos/take.py:574 E (and 61 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2C0TvK6wCO8hoGRAQsAAEEPAoU=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') __________ test_three_in_a_row[strandedness_chain126-method_chain126] __________ [gw7] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', 'opposite') method_chain = ('intersect', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('intersect', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/attr.py:65 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:17 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:21 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:37 E (and 91 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BAAEYGTAAAADQAAg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') __________ test_three_in_a_row[strandedness_chain187-method_chain187] __________ [gw6] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', False) method_chain = ('subtract', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('subtract', 'subtract'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:30 E (and 19 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4594263 | 4603817 | a | 0 | - | | chr1 | 2 | 2066 | a | 0 | - | | chr3 | 7462334 | 7462335 | a | 0 | + | | chr3 | 2889464 | 2890482 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4594263 | 4603817 | a | 0 | - | | chr1 | 2 | 2066 | a | 0 | - | | chr3 | 2889464 | 2889721 | a | 0 | + | | chr3 | 7462334 | 7462335 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2 | 2066 | a | 0 | + | | chr1 | 4594263 | 4603817 | a | 0 | - | | chr3 | 7462334 | 7462335 | a | 0 | - | | chr3 | 2889464 | 2890482 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2 | 2066 | a | 0 | + | | chr1 | 4594263 | 4603817 | a | 0 | - | | chr3 | 7462334 | 7462335 | a | 0 | - | | chr3 | 2889464 | 2889721 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2 | 2066 | a | 0 | + | | chr1 | 4594263 | 4603817 | a | 0 | - | | chr3 | 7462334 | 7462335 | a | 0 | - | | chr3 | 2889464 | 2889721 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4594263 | 4603817 | a | 0 | - | | chr1 | 2 | 2066 | a | 0 | - | | chr3 | 2889464 | 2889721 | a | 0 | + | | chr3 | 7462334 | 7462335 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4594263 | 4603817 | a | 0 | - | | chr1 | 2 | 2066 | a | 0 | - | | chr3 | 2889464 | 2889721 | a | 0 | + | | chr3 | 7462334 | 7462335 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4594263 | 4594520 | a | 0 | - | | chr1 | 2 | 2066 | a | 0 | - | | chr3 | 2889464 | 2889721 | a | 0 | + | | chr3 | 7462334 | 7462335 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4594263 | 4594520 | a | 0 | - | | chr1 | 2 | 2066 | a | 0 | - | | chr3 | 2889464 | 2889721 | a | 0 | + | | chr3 | 7462334 | 7462335 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4594263 | 4594264 | a | 0 | - | | chr1 | 2 | 2066 | a | 0 | - | | chr3 | 2889464 | 2889721 | a | 0 | + | | chr3 | 7462334 | 7462335 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4594263 | 4594264 | a | 0 | - | | chr1 | 2 | 259 | a | 0 | - | | chr3 | 2889464 | 2889721 | a | 0 | + | | chr3 | 7462334 | 7462335 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4594263 | 4594264 | a | 0 | - | | chr1 | 2 | 259 | a | 0 | - | | chr3 | 2889464 | 2889721 | a | 0 | + | | chr3 | 7462334 | 7462335 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4594263 | 4594264 | a | 0 | - | | chr1 | 2 | 259 | a | 0 | - | | chr3 | 2889464 | 2889721 | a | 0 | + | | chr3 | 7462334 | 7462335 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4594263 | 4594264 | a | 0 | - | | chr1 | 2 | 259 | a | 0 | - | | chr3 | 78 | 335 | a | 0 | + | | chr3 | 7462334 | 7462591 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4594263 | 4594264 | a | 0 | - | | chr1 | 2 | 259 | a | 0 | - | | chr3 | 78 | 335 | a | 0 | + | | chr3 | 7462334 | 7462591 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2 | 3 | a | 0 | - | | chr1 | 3 | 260 | a | 0 | - | | chr3 | 1 | 2 | a | 0 | - | | chr3 | 2 | 3 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2 | 3 | a | 0 | - | | chr1 | 2 | 259 | a | 0 | - | | chr3 | 7462334 | 7462335 | a | 0 | - | | chr3 | 2 | 3 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2 | 3 | a | 0 | - | | chr1 | 3 | 260 | a | 0 | - | | chr3 | 7462334 | 7462335 | a | 0 | - | | chr3 | 2 | 3 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2 | 3 | a | 0 | - | | chr1 | 3 | 260 | a | 0 | - | | chr3 | 1 | 2 | a | 0 | - | | chr3 | 2 | 3 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2 | 3 | a | 0 | - | | chr1 | 3 | 260 | a | 0 | - | | chr3 | 2 | 3 | a | 0 | - | | chr18 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2 | 3 | a | 0 | - | | chr1 | 3 | 260 | a | 0 | - | | chr3 | 2 | 3 | a | 0 | - | | chr18 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2 | 3 | a | 0 | - | | chr1 | 3 | 260 | a | 0 | - | | chr3 | 2 | 3 | a | 0 | - | | chr18 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2 | 3 | a | 0 | - | | chr1 | 3 | 260 | a | 0 | - | | chr2 | 2 | 3 | a | 0 | - | | chr18 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 257 | 258 | a | 0 | - | | chr1 | 1 | 258 | a | 0 | - | | chr1 | 257 | 258 | a | 0 | - | | chr1 | 257 | 258 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | | chr2 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | | chr2 | 1 | 2 | a | 0 | - | | chr3 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | | chr2 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 257 | 258 | a | 0 | - | | chr1 | 1 | 258 | a | 0 | - | | chr1 | 257 | 258 | a | 0 | - | | chr1 | 257 | 258 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 258 | a | 0 | - | | chr2 | 1 | 258 | a | 0 | - | | chr2 | 1 | 258 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 258 | a | 0 | - | | chr1 | 1 | 258 | a | 0 | - | | chr1 | 1 | 258 | a | 0 | - | | chr1 | 1 | 258 | a | 0 | - | | chr1 | 1 | 258 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 258 | a | 0 | - | | chr1 | 1 | 258 | a | 0 | - | | chr1 | 1 | 258 | a | 0 | - | | chr1 | 1 | 258 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 258 | a | 0 | - | | chr1 | 1 | 258 | a | 0 | - | | chr1 | 1 | 258 | a | 0 | - | | chr1 | 1 | 258 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr2 | 257 | 258 | a | 0 | - | | chr2 | 1 | 258 | a | 0 | - | | chr2 | 257 | 258 | a | 0 | - | | chr2 | 257 | 258 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr2 | 1 | 258 | a | 0 | + | | chr2 | 1 | 258 | a | 0 | + | | chr2 | 1 | 258 | a | 0 | + | | chr2 | 1 | 258 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr2 | 1 | 258 | a | 0 | - | | chr2 | 1 | 258 | a | 0 | - | | chr2 | 1 | 258 | a | 0 | - | | chr2 | 1 | 258 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr2 | 1 | 2 | a | 0 | - | | chr2 | 1 | 2 | a | 0 | - | | chr2 | 1 | 2 | a | 0 | - | | chr2 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr2 | 1 | 2 | a | 0 | - | | chr2 | 1 | 2 | a | 0 | - | | chr2 | 1 | 2 | a | 0 | - | | chr2 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr2 | 1 | 2 | a | 0 | - | | chr2 | 1 | 2 | a | 0 | - | | chr2 | 1 | 2 | a | 0 | - | | chr2 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr2 | 1 | 2 | a | 0 | - | | chr2 | 1 | 2 | a | 0 | - | | chr2 | 1 | 2 | a | 0 | - | | chr2 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 258 | a | 0 | - | | chr1 | 1 | 258 | a | 0 | - | | chr1 | 1 | 258 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr2 | 1 | 2 | a | 0 | - | | chr2 | 1 | 2 | a | 0 | - | | chr2 | 1 | 2 | a | 0 | - | | chr2 | 1 | 2 | a | 0 | - | | chr2 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr2 | 1 | 2 | a | 0 | - | | chr2 | 1 | 2 | a | 0 | - | | chr2 | 1 | 2 | a | 0 | - | | chr2 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | | chr2 | 1 | 2 | a | 0 | - | | chr2 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | | chr2 | 1 | 2 | a | 0 | - | | chr2 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | | chr2 | 1 | 2 | a | 0 | - | | chr2 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | | chr2 | 1 | 2 | a | 0 | - | | chr2 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | | chr2 | 1 | 2 | a | 0 | - | | chr2 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | | chr2 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | | chr2 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr2 | 1 | 2 | a | 0 | + | | chr2 | 1 | 2 | a | 0 | + | | chr2 | 1 | 2 | a | 0 | + | | chr2 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr2 | 1 | 2 | a | 0 | + | | chr2 | 1 | 2 | a | 0 | + | | chr2 | 1 | 2 | a | 0 | + | | chr2 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr2 | 1 | 2 | a | 0 | + | | chr2 | 1 | 2 | a | 0 | + | | chr2 | 1 | 2 | a | 0 | + | | chr2 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr2 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr2 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr2 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr2 | 1 | 2 | a | 0 | + | | chr2 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain176-method_chain176] __________ [gw1] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', False) method_chain = ('intersect', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('intersect', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:38 E (and 109 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') __________ test_three_in_a_row[strandedness_chain166-method_chain166] __________ [gw2] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', False), method_chain = ('overlap', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('overlap', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:15 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:369 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:373 E (and 23 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ___________ test_three_in_a_row[strandedness_chain74-method_chain74] ___________ [gw5] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', 'same'), method_chain = ('nearest', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('nearest', 'intersect'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr2 | 1 | 2 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr2 | 2 | 3 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:73 E (and 27 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2SAAEYGOGBkRBZjRJdmAAABBQAI') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain152-method_chain152] __________ [gw8] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', False) method_chain = ('set_union', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('set_union', 'subtract'), E gr=Empty PyRanges, # or any other generated value E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/init.py:174 E (and 203 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BAAEYGTAAAADQAAg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain139-method_chain139] __________ [gw3] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', 'opposite'), method_chain = ('subtract', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('subtract', 'join'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:30 E (and 19 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAI4AxkAAABSAAM=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +6 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 5 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 5 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 11 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 6 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +6 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 5 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 5 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 11 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 6 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') __________ test_three_in_a_row[strandedness_chain112-method_chain112] __________ [gw10] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', 'opposite') method_chain = ('overlap', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('overlap', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/attr.py:11 E (and 329 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ___________ test_three_in_a_row[strandedness_chain87-method_chain87] ___________ [gw4] linux -- Python 3.12.6 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 880, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1722, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', 'same'), | method_chain=('subtract', 'nearest'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=Empty PyRanges, | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 5604048 | 5604049 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:53 | (and 29 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY4zIYWQAAygFAZF5WlFxCgsYGQN8mXKBUkDJ+NCm8xBFAImwBkc=') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 4384, in subtract | other_clusters = other.merge(strand=strand) | ^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 347, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', 'same'), | method_chain=('subtract', 'nearest'), | gr=Empty PyRanges, | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=Empty PyRanges, # or any other generated value | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:143 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:30 | (and 19 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2CAA0YUCgIAAEAAAw==') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 258 | a | 0 | ... | | chr1 | 1 | 258 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') ('subtract', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain99-method_chain99] ___________ [gw9] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', 'opposite') method_chain = ('set_union', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('set_union', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E (and 122 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2DklpH/ystzjIGBkQETAAA09gId') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') __________ test_three_in_a_row[strandedness_chain127-method_chain127] __________ [gw7] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', 'opposite') method_chain = ('intersect', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('intersect', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:145 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 E (and 27 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkFDJIMhDzZGRgZAADKAUGAB2jATk=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') __________ test_three_in_a_row[strandedness_chain188-method_chain188] __________ [gw6] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', False), method_chain = ('subtract', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('subtract', 'join'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:30 E /usr/lib/python3/dist-packages/pandas/core/dtypes/missing.py:207 E (and 19 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +6 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 5493 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 11 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 6 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') _____________________________ test_coverage[False] _____________________________ [gw0] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness = False @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness", strandedness) tests/test_binary.py:207: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:238: in test_coverage result = gr.coverage(gr2, strandedness=strandedness) pyranges/pyranges.py:1341: in coverage other = other.merge(count=True, strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_coverage( E strandedness=False, E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., # or any other generated value E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2TABIxYxAAAZAAD') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp7efyoh1f/f1.bed -b /tmp/tmp7efyoh1f/f2.bed Chromosome Start End Name Score Strand 0 chr1 4015096 4018320 a 0 + 1 chr1 5178431 5185707 a 0 + 2 chrX 9539258 9544765 a 0 + Chromosome Start End Name Score Strand 0 chr2 3792832 3800218 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp05mim2o4/f1.bed -b /tmp/tmp05mim2o4/f2.bed Chromosome Start End Name Score Strand 0 chr1 3792832 3792833 a 0 - 1 chr1 3792832 3796677 a 0 - 2 chrX 3792832 3797327 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 7387 a 0 - 1 chr1 1 258 a 0 - 2 chr1 1 7387 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp1yzindee/f1.bed -b /tmp/tmp1yzindee/f2.bed Chromosome Start End Name Score Strand 0 chr1 3792832 3792833 a 0 - 1 chr1 3792832 3796677 a 0 - 2 chrX 3792832 3797327 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 7387 a 0 - 1 chr1 1 258 a 0 - 2 chr1 1 7387 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp2do43d5q/f1.bed -b /tmp/tmp2do43d5q/f2.bed Chromosome Start End Name Score Strand 0 chr1 3792832 3792833 a 0 - 1 chr1 3792832 3796677 a 0 - 2 chrX 3792832 3797327 a 0 - Chromosome Start End Name Score Strand 0 chr1 3792832 3792833 a 0 - 1 chr1 3792832 3796677 a 0 - 2 chrX 3792832 3797327 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpjherjl6w/f1.bed -b /tmp/tmpjherjl6w/f2.bed Chromosome Start End Name Score Strand 0 chr1 3792832 3792833 a 0 - 1 chr1 3792832 3796677 a 0 - 2 chrX 3792832 3797327 a 0 - Chromosome Start End Name Score Strand 0 chr1 65537 65538 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpnk50f_hu/f1.bed -b /tmp/tmpnk50f_hu/f2.bed Chromosome Start End Name Score Strand 0 chr4 4285727 4287986 a 0 + 1 chr5 282249 289579 a 0 - 2 chr21 4381420 4390705 a 0 + 3 chr21 2155141 2162550 a 0 - 4 chr21 2155141 2157400 a 0 - 5 chr21 7813803 7815729 a 0 - 6 chr21 1203224 1203225 a 0 - 7 chr21 6027192 6029451 a 0 - 8 chr21 2866721 2868980 a 0 - 9 chr21 6615064 6616501 a 0 - 10 chr22 8843052 8845311 a 0 + Chromosome Start End Name Score Strand 0 chrY 850931 851922 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpk9a0ja2l/f1.bed -b /tmp/tmpk9a0ja2l/f2.bed Chromosome Start End Name Score Strand 0 chr22 65537 65538 a 0 + Chromosome Start End Name Score Strand 0 chr1 122 2381 a 0 + 1 chr1 2 12 a 0 - 2 chr1 2 2261 a 0 - 3 chr20 2 3 a 0 + 4 chr20 2 2261 a 0 + 5 chr20 2 2261 a 0 - 6 chr20 2 2261 a 0 - 7 chr20 2 3 a 0 - 8 chr20 2 4 a 0 - 9 chr20 2 2261 a 0 - 10 chr20 2 7332 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp3q_8_eu6/f1.bed -b /tmp/tmp3q_8_eu6/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpyal9egkx/f1.bed -b /tmp/tmpyal9egkx/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpu80f_rpr/f1.bed -b /tmp/tmpu80f_rpr/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpe_h5gi0f/f1.bed -b /tmp/tmpe_h5gi0f/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpaaj2gk44/f1.bed -b /tmp/tmpaaj2gk44/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpxgbs2tgn/f1.bed -b /tmp/tmpxgbs2tgn/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpp97hmqgf/f1.bed -b /tmp/tmpp97hmqgf/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpxr97hh_u/f1.bed -b /tmp/tmpxr97hh_u/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp44eq4kxt/f1.bed -b /tmp/tmp44eq4kxt/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 8564791 8568501 a 0 + 1 chr1 1870844 1874952 a 0 + 2 chr1 3080925 3086759 a 0 - 3 chr12 10000000 10007907 a 0 - 4 chr22 7328318 7329028 a 0 - 5 chrM 1200366 1207960 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpbj01nvpn/f1.bed -b /tmp/tmpbj01nvpn/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmphv9beo_t/f1.bed -b /tmp/tmphv9beo_t/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 3952437 3962140 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpw4wg2_fq/f1.bed -b /tmp/tmpw4wg2_fq/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp2nqg3r4q/f1.bed -b /tmp/tmp2nqg3r4q/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 2158125 2166475 a 0 + 1 chr11 1274647 1284062 a 0 + 2 chr11 4710164 4711130 a 0 + 3 chr11 3021360 3031149 a 0 + 4 chr11 2101504 2108229 a 0 + 5 chr11 915578 916949 a 0 + 6 chr11 2166483 2167496 a 0 + 7 chr11 5580951 5582853 a 0 - 8 chr11 3687132 3688990 a 0 - 9 chr11 5455003 5458694 a 0 - 10 chr11 3062574 3066460 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpvrmvm4ha/f1.bed -b /tmp/tmpvrmvm4ha/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp1fe40nih/f1.bed -b /tmp/tmp1fe40nih/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 6065311 6071880 a 0 + 1 chr1 6373092 6373232 a 0 + 2 chr1 5936055 5936195 a 0 + 3 chr1 6065311 6074973 a 0 + 4 chr1 6065311 6065451 a 0 + 5 chr1 3628327 3628467 a 0 - 6 chr1 8622515 8622655 a 0 - 7 chr17 6065311 6065451 a 0 + 8 chr19 6065311 6065451 a 0 + 9 chrM 1949773 1949913 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpfrmh6ocp/f1.bed -b /tmp/tmpfrmh6ocp/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpf8oqezdq/f1.bed -b /tmp/tmpf8oqezdq/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 9423548 9433547 a 0 - 1 chr1 2144440 2145304 a 0 - 2 chr7 6921218 6928433 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpqcsu1ogo/f1.bed -b /tmp/tmpqcsu1ogo/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp9sei4v_r/f1.bed -b /tmp/tmp9sei4v_r/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 9354754 9362160 a 0 - 1 chr7 166563 174625 a 0 - 2 chr8 3754342 3762364 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpijahmwdc/f1.bed -b /tmp/tmpijahmwdc/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpzynlnq0f/f1.bed -b /tmp/tmpzynlnq0f/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr6 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 4934904 4938808 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpqpp6ioq6/f1.bed -b /tmp/tmpqpp6ioq6/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr6 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp_2qqlf_l/f1.bed -b /tmp/tmp_2qqlf_l/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1538148 1544158 a 0 + 1 chr1 9578238 9580379 a 0 + 2 chr1 589446 592279 a 0 - 3 chr5 9279110 9284189 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpp75ijban/f1.bed -b /tmp/tmpp75ijban/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmptb00qimc/f1.bed -b /tmp/tmptb00qimc/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr22 6337198 6340045 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpfrusotkc/f1.bed -b /tmp/tmpfrusotkc/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmptyistvce/f1.bed -b /tmp/tmptyistvce/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1986782 1987372 a 0 - 1 chr1 2004484 2004824 a 0 - 2 chr5 8307609 8311293 a 0 + 3 chr6 7722272 7725577 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp8hiz0c6k/f1.bed -b /tmp/tmp8hiz0c6k/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpm916bw1n/f1.bed -b /tmp/tmpm916bw1n/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr9 3026698 3030812 a 0 + 1 chr10 8092411 8101195 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp11hvys4n/f1.bed -b /tmp/tmp11hvys4n/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp9sdgahqf/f1.bed -b /tmp/tmp9sdgahqf/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 7727670 7733165 a 0 + 1 chr1 3678773 3688241 a 0 + 2 chr1 6792983 6796742 a 0 + 3 chr1 7871890 7876664 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpnphi9rd1/f1.bed -b /tmp/tmpnphi9rd1/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp7wkx7okd/f1.bed -b /tmp/tmp7wkx7okd/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 4864294 4869886 a 0 + 1 chr1 3091849 3101696 a 0 - 2 chr1 2092949 2098549 a 0 - 3 chr1 1021429 1027721 a 0 - 4 chr4 3482710 3486396 a 0 + 5 chr8 1 3724 a 0 - 6 chr12 10000000 10002051 a 0 - 7 chr15 9848495 9855393 a 0 + 8 chr15 215247 221320 a 0 + 9 chr16 3902051 3904452 a 0 - 10 chrM 5445966 5451719 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp5q3d_5fh/f1.bed -b /tmp/tmp5q3d_5fh/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp_31n0nnv/f1.bed -b /tmp/tmp_31n0nnv/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 9281636 9283809 a 0 + 1 chr1 7840256 7846689 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp4_txsy9o/f1.bed -b /tmp/tmp4_txsy9o/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpxa7r6wk4/f1.bed -b /tmp/tmpxa7r6wk4/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 10000000 10009791 a 0 + 1 chr1 4573004 4580380 a 0 + 2 chr1 875298 882674 a 0 + 3 chr1 753037 760413 a 0 + 4 chr1 3519284 3524915 a 0 - 5 chr5 5473360 5480736 a 0 - 6 chr9 1427582 1434958 a 0 + 7 chr13 8731205 8738581 a 0 + 8 chr14 2445862 2453238 a 0 - 9 chr17 2624113 2631489 a 0 - 10 chr22 5763256 5770632 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp2mtc5uhe/f1.bed -b /tmp/tmp2mtc5uhe/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpwv409g8d/f1.bed -b /tmp/tmpwv409g8d/f2.bed Chromosome Start End Name Score Strand 0 chr4 6132956 6132957 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 4381 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpi968g5nl/f1.bed -b /tmp/tmpi968g5nl/f2.bed Chromosome Start End Name Score Strand 0 chr4 6132956 6132957 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpbd9y7rp5/f1.bed -b /tmp/tmpbd9y7rp5/f2.bed Chromosome Start End Name Score Strand 0 chr1 2218838 2218915 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 248 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmprftq7zds/f1.bed -b /tmp/tmprftq7zds/f2.bed Chromosome Start End Name Score Strand 0 chr1 2218838 2218915 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp91zfdhw4/f1.bed -b /tmp/tmp91zfdhw4/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 8401528 8411495 a 0 - 1 chrM 8401528 8410110 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpfm5pfhcx/f1.bed -b /tmp/tmpfm5pfhcx/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmps0cl5l7e/f1.bed -b /tmp/tmps0cl5l7e/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 65537 65538 a 0 + Chromosome Start End Name Score Strand 0 chr9 2058564 2067067 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp67o8j1qd/f1.bed -b /tmp/tmp67o8j1qd/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 65537 65538 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp2yleytn5/f1.bed -b /tmp/tmp2yleytn5/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 6431181 6441181 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp_n1ofblh/f1.bed -b /tmp/tmp_n1ofblh/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpenc6qdr6/f1.bed -b /tmp/tmpenc6qdr6/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 9642323 9652006 a 0 - 1 chr2 928668 934065 a 0 + 2 chr7 8449814 8453633 a 0 - 3 chr7 2429301 2431594 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpf6qah3qa/f1.bed -b /tmp/tmpf6qah3qa/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpwwwonnk9/f1.bed -b /tmp/tmpwwwonnk9/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 8511298 8515187 a 0 + 1 chr1 8234070 8239869 a 0 + 2 chr1 2032344 2032345 a 0 - 3 chr1 3051385 3054959 a 0 - 4 chr2 7876238 7880703 a 0 - 5 chr9 725114 729163 a 0 + 6 chr18 8404464 8404828 a 0 - 7 chr21 4443634 4453429 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpwqsdgs4s/f1.bed -b /tmp/tmpwqsdgs4s/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmphjylhk1a/f1.bed -b /tmp/tmphjylhk1a/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 3116756 3120357 a 0 + 1 chr1 2230629 2239141 a 0 + 2 chr1 4501583 4509395 a 0 + 3 chr1 2331099 2337738 a 0 + 4 chr1 594820 597035 a 0 + 5 chr1 3252837 3254310 a 0 + 6 chr1 8383115 8384842 a 0 - 7 chr1 10000000 10002804 a 0 - 8 chr1 473789 476195 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpo_j7ce41/f1.bed -b /tmp/tmpo_j7ce41/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmps7tka6cw/f1.bed -b /tmp/tmps7tka6cw/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + 4 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr6 5109037 5110412 a 0 + 1 chr11 5109037 5117165 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpi8zez0aw/f1.bed -b /tmp/tmpi8zez0aw/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + 4 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpnma42ie4/f1.bed -b /tmp/tmpnma42ie4/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1815395 1824728 a 0 - 1 chr1 2031055 2036111 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpwrlpblr5/f1.bed -b /tmp/tmpwrlpblr5/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpvlarketr/f1.bed -b /tmp/tmpvlarketr/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 9164254 9168677 a 0 - 1 chr7 4597794 4602217 a 0 - 2 chr18 2392393 2397885 a 0 + 3 chr19 9806502 9807810 a 0 + 4 chr21 8747805 8755924 a 0 + 5 chr21 786890 794790 a 0 + 6 chr21 1051910 1058232 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpt_yia7ds/f1.bed -b /tmp/tmpt_yia7ds/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpnmwd_z0i/f1.bed -b /tmp/tmpnmwd_z0i/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 153159 155158 a 0 + 1 chr1 4180958 4185958 a 0 + 2 chr1 8487083 8492149 a 0 + 3 chr1 9417552 9424806 a 0 + 4 chr1 492052 493533 a 0 + 5 chr1 1329098 1332084 a 0 + 6 chr1 9375482 9382999 a 0 + 7 chr2 3714648 3717187 a 0 + 8 chr9 2170063 2179431 a 0 + 9 chr19 5522369 5526336 a 0 + 10 chrX 6837636 6844976 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpnahhgjm2/f1.bed -b /tmp/tmpnahhgjm2/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp5znmlo33/f1.bed -b /tmp/tmp5znmlo33/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 626338 632217 a 0 + 1 chr1 6355456 6355458 a 0 + 2 chr1 626338 629844 a 0 + 3 chr1 626338 628127 a 0 + 4 chr1 626338 634166 a 0 + 5 chr1 626338 635030 a 0 + 6 chr1 626338 630037 a 0 - 7 chr9 1421000 1423156 a 0 - 8 chr17 917381 919872 a 0 - 9 chr20 9290440 9298074 a 0 + 10 chrM 626338 628602 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp_ap4hswh/f1.bed -b /tmp/tmp_ap4hswh/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpxdv3gfev/f1.bed -b /tmp/tmpxdv3gfev/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 6766346 6775386 a 0 - 1 chr1 9459471 9468511 a 0 - 2 chr1 36886 45926 a 0 - 3 chr14 9459471 9468511 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpqfsgdbxo/f1.bed -b /tmp/tmpqfsgdbxo/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmptvpv0dnd/f1.bed -b /tmp/tmptvpv0dnd/f2.bed Chromosome Start End Name Score Strand 0 chr1 65537 65538 a 0 + Chromosome Start End Name Score Strand 0 chr1 1526201 1531821 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpke4fg7jq/f1.bed -b /tmp/tmpke4fg7jq/f2.bed Chromosome Start End Name Score Strand 0 chr1 65537 65538 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmps480uc4z/f1.bed -b /tmp/tmps480uc4z/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 7071000 7074562 a 0 + 1 chr1 2853686 2862961 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpn260vti7/f1.bed -b /tmp/tmpn260vti7/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpg1qfs9a5/f1.bed -b /tmp/tmpg1qfs9a5/f2.bed Chromosome Start End Name Score Strand 0 chr1 2635079 2635080 a 0 + Chromosome Start End Name Score Strand 0 chr1 87 88 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp3o1fb_xo/f1.bed -b /tmp/tmp3o1fb_xo/f2.bed Chromosome Start End Name Score Strand 0 chr1 2635079 2635080 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpq3v8ss2f/f1.bed -b /tmp/tmpq3v8ss2f/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 7404931 7408286 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpki6jwu6j/f1.bed -b /tmp/tmpki6jwu6j/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpqh8bzhkt/f1.bed -b /tmp/tmpqh8bzhkt/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr2 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 5408224 5415581 a 0 + 1 chr1 4588099 4595580 a 0 + 2 chr1 9959011 9960568 a 0 + 3 chr1 7459149 7459543 a 0 + 4 chr1 8409833 8412191 a 0 - 5 chr1 7437090 7446107 a 0 - 6 chr1 676480 677249 a 0 - 7 chr14 2621894 2621907 a 0 + 8 chr14 3432048 3432386 a 0 - 9 chrM 8458642 8459884 a 0 - 10 chrX 5939356 5944494 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmphufmby7v/f1.bed -b /tmp/tmphufmby7v/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr2 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpddh5u8vw/f1.bed -b /tmp/tmpddh5u8vw/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 120670 129110 a 0 + 1 chr1 2 5939 a 0 - 2 chr3 8318832 8323331 a 0 - 3 chr3 2721990 2725413 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpc7iiig8w/f1.bed -b /tmp/tmpc7iiig8w/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpkhifihc5/f1.bed -b /tmp/tmpkhifihc5/f2.bed Chromosome Start End Name Score Strand 0 chr12 1570050 1570051 a 0 + Chromosome Start End Name Score Strand 0 chr1 132 6630 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpg14cqdn4/f1.bed -b /tmp/tmpg14cqdn4/f2.bed Chromosome Start End Name Score Strand 0 chr12 1570050 1570051 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp88pdxfyx/f1.bed -b /tmp/tmp88pdxfyx/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 9024036 9028688 a 0 + 1 chr1 8974042 8982001 a 0 - 2 chr1 9329935 9334587 a 0 - 3 chr1 4310925 4319141 a 0 - 4 chr3 8667424 8675449 a 0 - 5 chr5 1635028 1644958 a 0 + 6 chr6 8714085 8721114 a 0 - 7 chr7 8496199 8500851 a 0 - 8 chr13 2280842 2285494 a 0 - 9 chr21 1027213 1027214 a 0 - 10 chrM 9553010 9561711 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpf02utssu/f1.bed -b /tmp/tmpf02utssu/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp5453daaf/f1.bed -b /tmp/tmp5453daaf/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 297402 305913 a 0 + 1 chr1 847213 853241 a 0 + 2 chr1 8081759 8087469 a 0 + 3 chr1 8081759 8081760 a 0 + 4 chr1 8081759 8088901 a 0 - 5 chr1 7993419 8001692 a 0 - 6 chr3 8081759 8084912 a 0 - 7 chr10 5879257 5884304 a 0 + 8 chr10 2553362 2563301 a 0 - 9 chr15 2638438 2644866 a 0 - 10 chr21 5261852 5264046 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp06b3g465/f1.bed -b /tmp/tmp06b3g465/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpw3zvvq2p/f1.bed -b /tmp/tmpw3zvvq2p/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 2003425 2011702 a 0 + 1 chr1 394181 404030 a 0 - 2 chr10 4420316 4425045 a 0 - 3 chr20 4420316 4428048 a 0 + 4 chr21 6783497 6790822 a 0 + 5 chr22 3598519 3603248 a 0 + 6 chrM 1706666 1707715 a 0 + 7 chrX 1299361 1309135 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmph66wxtty/f1.bed -b /tmp/tmph66wxtty/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp_kgtswjg/f1.bed -b /tmp/tmp_kgtswjg/f2.bed Chromosome Start End Name Score Strand 0 chr1 5436935 5436936 a 0 + Chromosome Start End Name Score Strand 0 chr1 25643 26127 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpigm2p_bw/f1.bed -b /tmp/tmpigm2p_bw/f2.bed Chromosome Start End Name Score Strand 0 chr1 5436935 5436936 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpfzavv4ke/f1.bed -b /tmp/tmpfzavv4ke/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 10001 a 0 + 1 chr1 4821492 4822782 a 0 + 2 chr1 7722756 7725221 a 0 + 3 chr1 9837845 9843606 a 0 + 4 chr1 6723846 6728786 a 0 + 5 chr4 30274 30275 a 0 + 6 chr10 3522007 3529046 a 0 + 7 chr14 1300834 1307412 a 0 + 8 chr17 4232271 4240675 a 0 + 9 chr18 5022199 5029513 a 0 - 10 chr19 8964863 8971180 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp2__yy2xs/f1.bed -b /tmp/tmp2__yy2xs/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp3kxftn8x/f1.bed -b /tmp/tmp3kxftn8x/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 7433291 7434367 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp6f7fyjif/f1.bed -b /tmp/tmp6f7fyjif/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpa0aphmy7/f1.bed -b /tmp/tmpa0aphmy7/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 4380270 4382146 a 0 + 1 chr1 7062085 7066536 a 0 - 2 chr1 9756907 9762161 a 0 - 3 chr11 7788621 7796499 a 0 - 4 chr15 4353876 4356821 a 0 - 5 chrY 7125935 7132492 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp9lou7jyv/f1.bed -b /tmp/tmp9lou7jyv/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpsol9mhnz/f1.bed -b /tmp/tmpsol9mhnz/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 868592 873711 a 0 + 1 chr1 1188981 1190822 a 0 + 2 chr1 4085747 4092635 a 0 + 3 chr1 9999999 10000000 a 0 - 4 chr1 3972477 3977630 a 0 - 5 chr1 8930940 8936059 a 0 - 6 chr1 5542346 5549650 a 0 - 7 chr1 7267695 7270380 a 0 - 8 chr5 9999999 10000966 a 0 - 9 chr10 758268 762616 a 0 - 10 chr20 3563167 3564343 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpfdpmksyz/f1.bed -b /tmp/tmpfdpmksyz/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp1kj9q494/f1.bed -b /tmp/tmp1kj9q494/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + 4 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 7392286 7399615 a 0 - 1 chr2 7337637 7337651 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpogib75th/f1.bed -b /tmp/tmpogib75th/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + 4 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpalpbkwwr/f1.bed -b /tmp/tmpalpbkwwr/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 5646113 5655486 a 0 + 1 chr1 5646113 5652775 a 0 - 2 chr1 1420340 1430340 a 0 - 3 chr17 4588717 4593377 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpgv9jb9b2/f1.bed -b /tmp/tmpgv9jb9b2/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpjvu6fzd4/f1.bed -b /tmp/tmpjvu6fzd4/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 3266111 3272035 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpkso50oyq/f1.bed -b /tmp/tmpkso50oyq/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpveep5mnd/f1.bed -b /tmp/tmpveep5mnd/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 2008052 2009572 a 0 + 1 chr1 2595554 2604916 a 0 - 2 chr1 1366213 1368024 a 0 - 3 chr1 7086857 7093964 a 0 - 4 chr13 9190081 9199413 a 0 + 5 chr13 8221474 8231474 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpwb_dlme8/f1.bed -b /tmp/tmpwb_dlme8/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpuv26_c7g/f1.bed -b /tmp/tmpuv26_c7g/f2.bed Chromosome Start End Name Score Strand 0 chr10 7389225 7389226 a 0 + Chromosome Start End Name Score Strand 0 chr1 246 7913 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpuiybq75t/f1.bed -b /tmp/tmpuiybq75t/f2.bed Chromosome Start End Name Score Strand 0 chr10 7389225 7389226 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp1zzjk1dz/f1.bed -b /tmp/tmp1zzjk1dz/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + 4 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 2903362 2905929 a 0 + 1 chr1 9143794 9144398 a 0 + 2 chr1 7358875 7366642 a 0 - 3 chr3 6202397 6211936 a 0 - 4 chr18 9704125 9710240 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp8tubqnz2/f1.bed -b /tmp/tmp8tubqnz2/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + 4 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpy4r7sxgn/f1.bed -b /tmp/tmpy4r7sxgn/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 989739 997069 a 0 + 1 chr1 8689502 8695075 a 0 + 2 chr1 294005 302064 a 0 + 3 chr1 4825801 4827199 a 0 + 4 chr1 8689502 8694165 a 0 - 5 chr1 8654951 8655726 a 0 - 6 chr4 8607945 8616304 a 0 - 7 chr7 8689502 8693356 a 0 - 8 chr9 4272294 4276466 a 0 - 9 chr13 7052253 7054560 a 0 - 10 chr14 2103252 2107291 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmputvikj8h/f1.bed -b /tmp/tmputvikj8h/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp5q56r2us/f1.bed -b /tmp/tmp5q56r2us/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 627365 627860 a 0 + 1 chr1 627365 637228 a 0 + 2 chr1 5308919 5313957 a 0 + 3 chr1 875690 876152 a 0 + 4 chr1 8676540 8686540 a 0 + 5 chr1 248782 257762 a 0 - 6 chr1 627365 628702 a 0 - 7 chr7 627365 632455 a 0 - 8 chr10 627365 637365 a 0 + 9 chr13 627365 630430 a 0 + 10 chr19 627365 629078 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp99wsxhmm/f1.bed -b /tmp/tmp99wsxhmm/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpgl8lmxnu/f1.bed -b /tmp/tmpgl8lmxnu/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + 4 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 108993 108995 a 0 + 1 chr12 865698 871524 a 0 + 2 chr18 7531705 7537781 a 0 + 3 chrX 429260 436970 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpj76nsfd1/f1.bed -b /tmp/tmpj76nsfd1/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + 4 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpvzm7f4l2/f1.bed -b /tmp/tmpvzm7f4l2/f2.bed Chromosome Start End Name Score Strand 0 chr1 408168 408425 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 6337 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpqmbw9r3e/f1.bed -b /tmp/tmpqmbw9r3e/f2.bed Chromosome Start End Name Score Strand 0 chr1 408168 408425 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp5b8kjqo8/f1.bed -b /tmp/tmp5b8kjqo8/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 7678271 7682339 a 0 + 1 chr1 8468325 8474814 a 0 + 2 chr1 4402283 4405068 a 0 + 3 chr1 1786088 1787963 a 0 - 4 chr8 6768119 6772973 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpno2yo7t6/f1.bed -b /tmp/tmpno2yo7t6/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpue7pk68r/f1.bed -b /tmp/tmpue7pk68r/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 9154152 9156792 a 0 + 1 chr1 7278646 7288280 a 0 + 2 chr8 453330 457105 a 0 - 3 chrX 6150226 6156528 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmptua5zej_/f1.bed -b /tmp/tmptua5zej_/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpyd6bhxxd/f1.bed -b /tmp/tmpyd6bhxxd/f2.bed Chromosome Start End Name Score Strand 0 chrY 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp90w859ro/f1.bed -b /tmp/tmp90w859ro/f2.bed Chromosome Start End Name Score Strand 0 chrY 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp7_r_t318/f1.bed -b /tmp/tmp7_r_t318/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 8773686 8781984 a 0 + 1 chr1 895399 897172 a 0 - 2 chr1 9984642 9986749 a 0 - 3 chr1 941835 946051 a 0 - 4 chr10 3683140 3683759 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpc9legiy8/f1.bed -b /tmp/tmpc9legiy8/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpp0e8cqb1/f1.bed -b /tmp/tmpp0e8cqb1/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 5143645 5150613 a 0 + 1 chr1 1466125 1473093 a 0 + 2 chr1 9851560 9858528 a 0 + 3 chr1 2230532 2237500 a 0 + 4 chr1 493459 500427 a 0 + 5 chr2 3746763 3753731 a 0 - 6 chr10 5729349 5736317 a 0 + 7 chr10 5591482 5598450 a 0 - 8 chr14 2998349 3005317 a 0 + 9 chr20 9709788 9716756 a 0 + 10 chr21 9709788 9716756 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpc1cctfpl/f1.bed -b /tmp/tmpc1cctfpl/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpuxuhjwho/f1.bed -b /tmp/tmpuxuhjwho/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 8887461 8896389 a 0 + 1 chr6 5160923 5163375 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpcdj1cxeg/f1.bed -b /tmp/tmpcdj1cxeg/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp4n5wim97/f1.bed -b /tmp/tmp4n5wim97/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr3 297784 299279 a 0 - 1 chr19 7080465 7090465 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpb553mv8_/f1.bed -b /tmp/tmpb553mv8_/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmppfqz3y_8/f1.bed -b /tmp/tmppfqz3y_8/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 8999664 9001863 a 0 + 1 chr1 6517879 6521797 a 0 - 2 chr3 5910441 5914443 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpx87sqgin/f1.bed -b /tmp/tmpx87sqgin/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp0rrdb05q/f1.bed -b /tmp/tmp0rrdb05q/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr13 4858869 4859302 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp0mq3dxzg/f1.bed -b /tmp/tmp0mq3dxzg/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpgrhvdwee/f1.bed -b /tmp/tmpgrhvdwee/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 6401213 6407313 a 0 + 1 chr1 304905 312513 a 0 + 2 chr1 8544161 8546260 a 0 + 3 chr1 7376373 7381202 a 0 - 4 chr1 5213056 5217595 a 0 - 5 chr12 10000000 10007429 a 0 + 6 chr14 2955349 2956334 a 0 + 7 chr16 7092736 7095053 a 0 + 8 chr19 1661654 1664191 a 0 + 9 chr21 7758338 7758340 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmphjhc7s6v/f1.bed -b /tmp/tmphjhc7s6v/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpj3u9yd1p/f1.bed -b /tmp/tmpj3u9yd1p/f2.bed Chromosome Start End Name Score Strand 0 chr1 6947073 6947074 a 0 + Chromosome Start End Name Score Strand 0 chr1 2728967 2733045 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpnsdl68cw/f1.bed -b /tmp/tmpnsdl68cw/f2.bed Chromosome Start End Name Score Strand 0 chr1 6947073 6947074 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpz2io9g93/f1.bed -b /tmp/tmpz2io9g93/f2.bed Chromosome Start End Name Score Strand 0 chr2 9830657 9830658 a 0 + Chromosome Start End Name Score Strand 0 chr1 862150 864440 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpia4z6vq7/f1.bed -b /tmp/tmpia4z6vq7/f2.bed Chromosome Start End Name Score Strand 0 chr2 9830657 9830658 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpzm4mmf1i/f1.bed -b /tmp/tmpzm4mmf1i/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr2 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 3528736 3533993 a 0 + 1 chr1 6184563 6185472 a 0 + 2 chr1 5058386 5058926 a 0 - 3 chr3 157007 159276 a 0 - 4 chr3 8223201 8229657 a 0 - 5 chr3 5706184 5711820 a 0 - 6 chr7 6490041 6497734 a 0 + 7 chr9 7195757 7196444 a 0 + 8 chr12 8009331 8009798 a 0 - 9 chr19 8805257 8810280 a 0 - 10 chr19 3872612 3879483 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp8quqz04u/f1.bed -b /tmp/tmp8quqz04u/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr2 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpj58dgjr3/f1.bed -b /tmp/tmpj58dgjr3/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 6740870 6743136 a 0 + 1 chr1 6950554 6957417 a 0 + 2 chr1 1619420 1620329 a 0 + 3 chr1 4134456 4136722 a 0 - 4 chr1 6740870 6740871 a 0 - 5 chr5 8164994 8174860 a 0 + 6 chr19 9495135 9497401 a 0 + 7 chr19 9004626 9008406 a 0 + 8 chr19 4653270 4657246 a 0 - 9 chr19 7533045 7535489 a 0 - 10 chr20 3971581 3979216 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpt7xsfpua/f1.bed -b /tmp/tmpt7xsfpua/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpqoml2q17/f1.bed -b /tmp/tmpqoml2q17/f2.bed Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 + 1 chr12 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr16 2869993 2875898 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpaebnb62c/f1.bed -b /tmp/tmpaebnb62c/f2.bed Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 + 1 chr12 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpplagbw_a/f1.bed -b /tmp/tmpplagbw_a/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1322273 1328897 a 0 + 1 chr13 6662342 6666625 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpxc5zluvk/f1.bed -b /tmp/tmpxc5zluvk/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp01zxz0ow/f1.bed -b /tmp/tmp01zxz0ow/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 3729149 3738971 a 0 + 1 chr1 2156280 2164756 a 0 + 2 chr1 8848779 8858513 a 0 - 3 chr1 3382348 3382473 a 0 - 4 chr16 8679342 8687894 a 0 + 5 chr16 6698689 6705121 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpxisdnhd9/f1.bed -b /tmp/tmpxisdnhd9/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmplv4zs6uu/f1.bed -b /tmp/tmplv4zs6uu/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 4462623 4469849 a 0 + 1 chr1 5863570 5870796 a 0 + 2 chr1 698878 707693 a 0 - 3 chr1 6501974 6510680 a 0 - 4 chr3 719629 723646 a 0 - 5 chr6 5664522 5674456 a 0 - 6 chr10 2369813 2372858 a 0 - 7 chr22 2651676 2658902 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpv6g6_1q3/f1.bed -b /tmp/tmpv6g6_1q3/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpsar62bbo/f1.bed -b /tmp/tmpsar62bbo/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 - 1 chr6 5452993 5462993 a 0 - 2 chr22 163993 164975 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp17_qqzp7/f1.bed -b /tmp/tmp17_qqzp7/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpesx2jm0a/f1.bed -b /tmp/tmpesx2jm0a/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr13 1 9610 a 0 + 1 chr14 9501426 9504586 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpxnz9n2i6/f1.bed -b /tmp/tmpxnz9n2i6/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp8ne5vjps/f1.bed -b /tmp/tmp8ne5vjps/f2.bed Chromosome Start End Name Score Strand 0 chr1 5989395 5989652 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 3175 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp4335gr3h/f1.bed -b /tmp/tmp4335gr3h/f2.bed Chromosome Start End Name Score Strand 0 chr1 5989395 5989652 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpy_7r5ufq/f1.bed -b /tmp/tmpy_7r5ufq/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 6425099 6425421 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpj5_ddp0t/f1.bed -b /tmp/tmpj5_ddp0t/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpkkkegbgs/f1.bed -b /tmp/tmpkkkegbgs/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 8488948 8491117 a 0 + 1 chr1 7449684 7452353 a 0 + 2 chr1 4793974 4800812 a 0 + 3 chr1 9133113 9135521 a 0 - 4 chr2 7556798 7556799 a 0 + 5 chr5 4375778 4382261 a 0 + 6 chr5 10000000 10001799 a 0 - 7 chr6 7666089 7670654 a 0 - 8 chr14 8218427 8221860 a 0 - 9 chr15 7770753 7773497 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpzhvj3pzy/f1.bed -b /tmp/tmpzhvj3pzy/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmprwnet17s/f1.bed -b /tmp/tmprwnet17s/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 6079748 6088900 a 0 + 1 chr1 6079748 6089105 a 0 + 2 chr1 6079748 6088954 a 0 + 3 chr1 6079748 6089105 a 0 - 4 chr2 6079748 6088058 a 0 - 5 chr7 1727337 1733475 a 0 + 6 chr11 6079748 6089105 a 0 - 7 chr12 6079748 6089409 a 0 + 8 chr14 6079748 6081581 a 0 - 9 chrM 6079748 6089105 a 0 + 10 chrM 5087028 5096329 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp2waiokzg/f1.bed -b /tmp/tmp2waiokzg/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpj2pie7uk/f1.bed -b /tmp/tmpj2pie7uk/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr6 3111736 3111737 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpemge8pfd/f1.bed -b /tmp/tmpemge8pfd/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpnrf44e8h/f1.bed -b /tmp/tmpnrf44e8h/f2.bed Chromosome Start End Name Score Strand 0 chr1 7393041 7393298 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 259 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpk5yz8gug/f1.bed -b /tmp/tmpk5yz8gug/f2.bed Chromosome Start End Name Score Strand 0 chr1 7393041 7393298 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp8eg5d89h/f1.bed -b /tmp/tmp8eg5d89h/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1127148 1128304 a 0 + 1 chr1 1213919 1213922 a 0 - 2 chr1 7987975 7988016 a 0 - 3 chr1 5300452 5300872 a 0 - 4 chr3 5839672 5845915 a 0 - 5 chr7 2054277 2054279 a 0 + 6 chr16 7628364 7636752 a 0 - 7 chr21 4885255 4885421 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmphm7mc444/f1.bed -b /tmp/tmphm7mc444/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp51a89w1g/f1.bed -b /tmp/tmp51a89w1g/f2.bed Chromosome Start End Name Score Strand 0 chr13 2482250 2482251 a 0 + Chromosome Start End Name Score Strand 0 chr1 108 3001 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpkyho3bpj/f1.bed -b /tmp/tmpkyho3bpj/f2.bed Chromosome Start End Name Score Strand 0 chr13 2482250 2482251 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpzp0ywirx/f1.bed -b /tmp/tmpzp0ywirx/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr2 164029 166834 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpj3bae6lu/f1.bed -b /tmp/tmpj3bae6lu/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmph93tzv3q/f1.bed -b /tmp/tmph93tzv3q/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 5694315 5703582 a 0 + 1 chr6 1508609 1516886 a 0 - 2 chr21 3215060 3224425 a 0 + 3 chr21 3584487 3593852 a 0 + 4 chr21 7489649 7495217 a 0 + 5 chr21 6158182 6167547 a 0 - 6 chr21 4538116 4548115 a 0 - 7 chr21 4979077 4983963 a 0 - 8 chr21 754921 764286 a 0 - 9 chr21 1508609 1517974 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpav3z_bxq/f1.bed -b /tmp/tmpav3z_bxq/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpdne1eudn/f1.bed -b /tmp/tmpdne1eudn/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr5 6568553 6575227 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpqrtp_pgg/f1.bed -b /tmp/tmpqrtp_pgg/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpp0xn5z8t/f1.bed -b /tmp/tmpp0xn5z8t/f2.bed Chromosome Start End Name Score Strand 0 chr20 5334617 5334618 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 9951 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmptsnvl20i/f1.bed -b /tmp/tmptsnvl20i/f2.bed Chromosome Start End Name Score Strand 0 chr20 5334617 5334618 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpao704mbm/f1.bed -b /tmp/tmpao704mbm/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 2961398 2969206 a 0 + 1 chr1 5377559 5384656 a 0 + 2 chr20 1385559 1386295 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp31g2q3j6/f1.bed -b /tmp/tmp31g2q3j6/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpkqmc6e84/f1.bed -b /tmp/tmpkqmc6e84/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 6551779 6552814 a 0 + 1 chr1 1 5313 a 0 - 2 chr1 6364206 6373811 a 0 - 3 chr1 2449651 2455453 a 0 - 4 chr10 3661807 3663047 a 0 - 5 chr11 5313487 5318355 a 0 + 6 chr11 6364206 6371411 a 0 - 7 chr13 8959614 8967411 a 0 + 8 chr14 6911476 6918215 a 0 - 9 chr16 335969 335970 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpoc1bn_qv/f1.bed -b /tmp/tmpoc1bn_qv/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpue3z01r_/f1.bed -b /tmp/tmpue3z01r_/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chrY 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr18 7786657 7793485 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp1yytubvc/f1.bed -b /tmp/tmp1yytubvc/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chrY 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp4e6nk_kw/f1.bed -b /tmp/tmp4e6nk_kw/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1752834 1753961 a 0 + 1 chr1 4980938 4985290 a 0 + 2 chr10 9353540 9355213 a 0 + 3 chrM 4651097 4657358 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpzlaeyph8/f1.bed -b /tmp/tmpzlaeyph8/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpdjv5_y3r/f1.bed -b /tmp/tmpdjv5_y3r/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr20 4626361 4635589 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpaytufmo3/f1.bed -b /tmp/tmpaytufmo3/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmppacr1i0i/f1.bed -b /tmp/tmppacr1i0i/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 8582028 8586740 a 0 + 1 chr1 9071765 9081201 a 0 + 2 chr2 150916 152213 a 0 + 3 chr2 6887943 6892708 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpadqifls9/f1.bed -b /tmp/tmpadqifls9/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp0f16uynt/f1.bed -b /tmp/tmp0f16uynt/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1709722 1710506 a 0 + 1 chr1 4184903 4188757 a 0 + 2 chr1 9999999 10004941 a 0 + 3 chr1 8598572 8603665 a 0 - 4 chr1 1723084 1725082 a 0 - 5 chr4 9758655 9760629 a 0 + 6 chr7 7973726 7979841 a 0 + 7 chr9 7813511 7821187 a 0 - 8 chr12 5945885 5951030 a 0 - 9 chr20 5421147 5426499 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpyngjsu7z/f1.bed -b /tmp/tmpyngjsu7z/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp8twx4vqd/f1.bed -b /tmp/tmp8twx4vqd/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 9223360 9223362 a 0 + 1 chr1 939999 944152 a 0 + 2 chr1 3756203 3759088 a 0 + 3 chr1 1187050 1193401 a 0 + 4 chr1 2441997 2445741 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpqillnuox/f1.bed -b /tmp/tmpqillnuox/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpmrttehdg/f1.bed -b /tmp/tmpmrttehdg/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 2278500 2279429 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmphewfl0xs/f1.bed -b /tmp/tmphewfl0xs/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmptv85ujh4/f1.bed -b /tmp/tmptv85ujh4/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr4 9221591 9222982 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp46a7kcpv/f1.bed -b /tmp/tmp46a7kcpv/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpbb03yuou/f1.bed -b /tmp/tmpbb03yuou/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 5333503 5335986 a 0 + 1 chr1 8903347 8904976 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpcfzar9yw/f1.bed -b /tmp/tmpcfzar9yw/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpqys7cy1d/f1.bed -b /tmp/tmpqys7cy1d/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 5718858 5725396 a 0 + 1 chr1 5438413 5445875 a 0 + 2 chr1 860266 866804 a 0 - 3 chr13 771473 772935 a 0 + 4 chr14 3212384 3218701 a 0 + 5 chrY 8322713 8327079 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp1e6zwuhh/f1.bed -b /tmp/tmp1e6zwuhh/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmphgronmzx/f1.bed -b /tmp/tmphgronmzx/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 7597012 7597013 a 0 - 1 chr1 6856181 6856668 a 0 - 2 chr3 405881 413655 a 0 + 3 chr22 6027772 6033804 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmplklg6vct/f1.bed -b /tmp/tmplklg6vct/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp_f4vavnc/f1.bed -b /tmp/tmp_f4vavnc/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 3074991 3080074 a 0 + 1 chr1 1728388 1738388 a 0 + 2 chr1 3616114 3622315 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp670b6x1q/f1.bed -b /tmp/tmp670b6x1q/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpbfpslzek/f1.bed -b /tmp/tmpbfpslzek/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 2962015 2962016 a 0 + 1 chr1 1470978 1472951 a 0 + 2 chr1 1470978 1479866 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp71htjd3w/f1.bed -b /tmp/tmp71htjd3w/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 2112269 2120396 a 0 + 1 chr1 7951441 7952324 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpfji0xog_/f1.bed -b /tmp/tmpfji0xog_/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 4809481 4816343 a 0 + 1 chr1 9610050 9610059 a 0 - 2 chr1 8806759 8808214 a 0 - 3 chr10 7333106 7341718 a 0 + 4 chr21 238268 246124 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp1tv68obt/f1.bed -b /tmp/tmp1tv68obt/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 8207200 8209457 a 0 + 1 chr1 3119523 3120889 a 0 - 2 chr1 4870142 4873150 a 0 - 3 chr3 7854291 7864228 a 0 - 4 chr8 5915227 5920044 a 0 + 5 chr11 8072325 8077351 a 0 + 6 chr11 7432937 7442656 a 0 + 7 chr11 5252234 5254256 a 0 + 8 chr11 738225 748162 a 0 - 9 chr13 4985737 4988064 a 0 + 10 chr16 1728803 1730430 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp8r3zdpim/f1.bed -b /tmp/tmp8r3zdpim/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chrX 3680873 3684013 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpf6qxjdxn/f1.bed -b /tmp/tmpf6qxjdxn/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 8557561 8559278 a 0 + 1 chr5 6470964 6478492 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmphytclzos/f1.bed -b /tmp/tmphytclzos/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 3833447 3835305 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmppi8nmb29/f1.bed -b /tmp/tmppi8nmb29/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 9999999 10000342 a 0 - 1 chr17 5779149 5785193 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpqy3j53w7/f1.bed -b /tmp/tmpqy3j53w7/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 8017103 8017247 a 0 - 1 chrY 967769 967889 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpg6e9rwb0/f1.bed -b /tmp/tmpg6e9rwb0/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1703108 1711582 a 0 - 1 chr2 9109172 9114587 a 0 - 2 chr5 6664171 6670351 a 0 - 3 chr7 9434800 9443274 a 0 - 4 chr15 5367836 5370464 a 0 - 5 chr16 5134819 5143293 a 0 - 6 chr21 3945238 3953712 a 0 + 7 chr21 2762770 2766198 a 0 + 8 chr21 4444053 4450534 a 0 + 9 chr22 6901992 6908965 a 0 - 10 chrY 9353212 9361686 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp3bszsv56/f1.bed -b /tmp/tmp3bszsv56/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1674785 1677106 a 0 + 1 chr1 9864998 9873143 a 0 + 2 chr1 6780585 6781138 a 0 - 3 chr18 110332 119888 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpj472pxr8/f1.bed -b /tmp/tmpj472pxr8/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 5157583 5160629 a 0 + 1 chr1 5157583 5159358 a 0 - 2 chr1 5157583 5166387 a 0 - 3 chr1 5157583 5161199 a 0 - 4 chr2 5157583 5165923 a 0 + 5 chr19 9875915 9878313 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpxtqdmxv0/f1.bed -b /tmp/tmpxtqdmxv0/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 6391468 6392330 a 0 + 1 chr1 2706573 2715239 a 0 + 2 chr1 10000000 10002986 a 0 + 3 chr1 5656465 5666187 a 0 + 4 chr1 5086603 5091858 a 0 + 5 chr1 4845593 4847001 a 0 - 6 chr1 5506271 5509021 a 0 - 7 chr1 9467722 9467723 a 0 - 8 chr10 5542767 5549958 a 0 + 9 chr12 851279 851281 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpy5zkulv2/f1.bed -b /tmp/tmpy5zkulv2/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 9628746 9632780 a 0 + 1 chr1 931692 941479 a 0 + 2 chr1 8636240 8636379 a 0 + 3 chr9 6793514 6795180 a 0 + 4 chr19 2 2728 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp5knd86r9/f1.bed -b /tmp/tmp5knd86r9/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 6909400 6912212 a 0 + 1 chr1 9395400 9404251 a 0 - 2 chr11 7090204 7099538 a 0 - 3 chr16 5096825 5100037 a 0 - 4 chr16 8597710 8597944 a 0 - 5 chr16 908707 909865 a 0 - 6 chr16 9030298 9039856 a 0 - 7 chr16 5058676 5063864 a 0 - 8 chr16 9098025 9105084 a 0 - 9 chr16 9999999 10000576 a 0 - 10 chr16 3257536 3260284 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp1ral2usn/f1.bed -b /tmp/tmp1ral2usn/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 3121992 3128030 a 0 - 1 chr1 8603540 8611354 a 0 - 2 chr1 6662292 6668658 a 0 - 3 chr1 8081329 8083265 a 0 - 4 chr1 242526 247544 a 0 - 5 chr1 181418 184525 a 0 - 6 chr1 5049683 5049806 a 0 - 7 chr2 3120317 3123255 a 0 + 8 chr9 1011819 1017075 a 0 - 9 chrM 6880843 6884745 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp1_2emvzw/f1.bed -b /tmp/tmp1_2emvzw/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 186279 186501 a 0 + 1 chr1 2766137 2770607 a 0 + 2 chr1 9489002 9493104 a 0 - 3 chr1 4308382 4315851 a 0 - 4 chr12 1311426 1316569 a 0 - 5 chr13 2 2464 a 0 - 6 chr22 7027936 7034035 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp1o_kaful/f1.bed -b /tmp/tmp1o_kaful/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr2 7094009 7097850 a 0 - 1 chr15 5381582 5388140 a 0 + 2 chr15 9296770 9306768 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp1fklo2ys/f1.bed -b /tmp/tmp1fklo2ys/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1958168 1967005 a 0 + 1 chr1 5868611 5874543 a 0 + 2 chr1 1620288 1621775 a 0 + 3 chr1 5868611 5871499 a 0 - 4 chr7 5868611 5869969 a 0 - 5 chr15 5868611 5868930 a 0 + 6 chr16 5868611 5869198 a 0 - 7 chrY 5005591 5013749 a 0 + 8 chrY 5868611 5869239 a 0 + 9 chrY 6922698 6924229 a 0 + 10 chrY 4317582 4321218 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpz4rhp1nw/f1.bed -b /tmp/tmpz4rhp1nw/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 2167816 2173009 a 0 + 1 chr1 222255 222519 a 0 + 2 chr1 4592792 4601376 a 0 - 3 chr1 7772446 7774682 a 0 - 4 chr1 9545504 9554929 a 0 - 5 chr9 5975203 5982755 a 0 - 6 chr10 8087555 8091619 a 0 + 7 chr11 1293278 1297860 a 0 - 8 chr17 9543255 9552976 a 0 - 9 chr21 4022371 4028533 a 0 - 10 chrX 3700241 3700461 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpybh4mees/f1.bed -b /tmp/tmpybh4mees/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 7425288 7432081 a 0 + 1 chr1 9433108 9441314 a 0 + 2 chr1 2557266 2565096 a 0 + 3 chr1 5389967 5398530 a 0 + 4 chr1 7595698 7602491 a 0 + 5 chr7 8967021 8967255 a 0 + 6 chr7 2841995 2848788 a 0 - 7 chr8 1981789 1988582 a 0 - 8 chr18 3462551 3466337 a 0 + 9 chr19 8217522 8227522 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpw5nq6iz6/f1.bed -b /tmp/tmpw5nq6iz6/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 3409361 3414677 a 0 + 1 chr1 1 3603 a 0 + 2 chr1 8202700 8212078 a 0 + 3 chr1 9398632 9401352 a 0 + 4 chr20 8914798 8916290 a 0 + 5 chr22 4975645 4976121 a 0 - 6 chrY 10000000 10007009 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp46_7kvma/f1.bed -b /tmp/tmp46_7kvma/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 5493484 5501367 a 0 + 1 chr1 5493484 5494271 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpqtip10il/f1.bed -b /tmp/tmpqtip10il/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 9431070 9432422 a 0 + 1 chr1 6159524 6163306 a 0 - 2 chr1 2349678 2356309 a 0 - 3 chrX 2046531 2047496 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp7ia_e981/f1.bed -b /tmp/tmp7ia_e981/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1002137 1004976 a 0 + 1 chr1 7828115 7829575 a 0 + 2 chr1 9456201 9456522 a 0 + 3 chr1 8689019 8693965 a 0 - 4 chr1 305409 306532 a 0 - 5 chr7 8970043 8970946 a 0 + 6 chrY 5408658 5409343 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpqjx5cyiw/f1.bed -b /tmp/tmpqjx5cyiw/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 6216056 6222438 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmplcvxwpfj/f1.bed -b /tmp/tmplcvxwpfj/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 5411962 5418865 a 0 + 1 chr1 2 5096 a 0 + 2 chr1 2 8606 a 0 + 3 chr1 6403433 6412865 a 0 - 4 chr1 2 7435 a 0 - 5 chr1 9532170 9538213 a 0 - 6 chr1 7549919 7551011 a 0 - 7 chr8 2 2836 a 0 - 8 chr16 4489841 4490658 a 0 - 9 chr22 1524757 1530747 a 0 + 10 chrY 2 3080 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpln206tpj/f1.bed -b /tmp/tmpln206tpj/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpglxw0dvp/f1.bed -b /tmp/tmpglxw0dvp/f2.bed ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain153-method_chain153] __________ [gw8] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', False), method_chain = ('set_union', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('set_union', 'join'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E (and 197 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2CAA0YGLAAAADUAAg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') __________ test_three_in_a_row[strandedness_chain100-method_chain100] __________ [gw9] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', 'opposite') method_chain = ('set_union', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('set_union', 'overlap'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E (and 186 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2CUZXNnYxXnYGBkwAIAD7kAlw==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') __________ test_three_in_a_row[strandedness_chain140-method_chain140] __________ [gw3] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', 'opposite'), method_chain = ('join', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('join', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/attr.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/attr.py:18 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/attr.py:20 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/attr.py:23 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/attr.py:28 E (and 214 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') __________ test_three_in_a_row[strandedness_chain113-method_chain113] __________ [gw10] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', 'opposite') method_chain = ('overlap', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('overlap', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:145 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 E /usr/lib/python3/dist-packages/pandas/core/dtypes/missing.py:207 E (and 18 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') __________ test_three_in_a_row[strandedness_chain178-method_chain178] __________ [gw1] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', False) method_chain = ('intersect', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:292: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('intersect', 'nearest'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E | chr1 | 1 | 2 | a | 0 | + | E | chr1 | 1 | 5870 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | + | E | chr1 | 2 | 3 | a | 0 | + | E | chr1 | 2 | 3 | a | 0 | + | E | chr1 | 2 | 3 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 4 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:53 E (and 29 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2RgYGBiBBKMIAJEMzDCSEZGCMHIyBQt9gYsApVE0cNY7mG9ECIKNwWqDyoKp8AAALmMAyE=') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3576960 | 3586960 | a | 0 | ... | | chr1 | 7003664 | 7009533 | a | 0 | ... | | chr1 | 3010493 | 3018663 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges 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('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 12 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain88-method_chain88] ___________ [gw4] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', 'same'), method_chain = ('subtract', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('subtract', 'intersect'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:30 E /usr/lib/python3/dist-packages/pandas/core/dtypes/missing.py:207 E (and 18 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 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('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ___________ test_three_in_a_row[strandedness_chain75-method_chain75] ___________ [gw5] linux -- Python 3.12.6 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 880, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1722, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', 'same'), | method_chain=('nearest', 'subtract'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=Empty PyRanges, | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:53 | (and 29 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2TABIxIFCOGLAAAqwAF') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 4384, in subtract | other_clusters = other.merge(strand=strand) | ^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 347, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', 'same'), | method_chain=('nearest', 'subtract'), | gr=Empty PyRanges, | gr2=Empty PyRanges, | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 258 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:143 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:30 | (and 19 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkYGBgY2RgYmQAsYAAwgCSYD4AAYQAEg==') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 258 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain198-method_chain198] __________ [gw0] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', 'same') method_chain = ('set_union', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('set_union', 'overlap'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E (and 196 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2DMCMrzkJVWZmBkwAIAMH4Bzg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') __________ test_three_in_a_row[strandedness_chain168-method_chain168] __________ [gw2] linux -- Python 3.12.6 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 880, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1722, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=('opposite', False), | method_chain=('nearest', 'set_union'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | | chr1 | 14 | 15 | a | 0 | - | | | chrX | 2543896 | 2543897 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 3 rows and 6 columns from 2 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=Empty PyRanges, | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | (and 170 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2QAA0YgBFMgwlz0zwPGMJUHWxlNHAJ+MzAyMQIRA4MYiAFSaKF2UZyRqRqklJGJgYEXrA8kBSKhBACybwgA') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3784, in set_union | gr = gr.merge(strand=strand) | ^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 360, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=('opposite', False), | method_chain=('nearest', 'set_union'), | gr=Empty PyRanges, | gr2=Empty PyRanges, # or any other generated value | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:33 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | (and 284 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain189-method_chain189] __________ [gw6] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', False), method_chain = ('join', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('join', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:33 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:41 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:17 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:21 E (and 96 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') __________ test_three_in_a_row[strandedness_chain101-method_chain101] __________ [gw9] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', 'opposite') method_chain = ('set_union', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('set_union', 'nearest'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E (and 183 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2CAA0YGLAAAADUAAg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') __________ test_three_in_a_row[strandedness_chain129-method_chain129] __________ [gw7] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', 'opposite') method_chain = ('intersect', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('intersect', 'nearest'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 258 | a | 0 | + | E | chr2 | 1 | 258 | a | 0 | + | E | chr2 | 1 | 258 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 3 rows and 6 columns from 2 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 65537 | 65538 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:53 E (and 29 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2RkAAJGBjAFAYxQzARmMMKEwKoYwSqhihlhKuHyKPoZAQVRABs=') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5640231 | 5647518 | a | 0 | ... | | chr1 | 5640231 | 5647980 | a | 0 | ... | | chr1 | 5640231 | 5647980 | a | 0 | ... | | chr1 | 5640231 | 5648448 | a | 0 | ... | | chr1 | 5640231 | 5647980 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 39 | 296 | a | 0 | ... | | chr1 | 39 | 296 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 258 | a | 0 | ... | | chr1 | 1 | 258 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 258 | a | 0 | ... | | chr1 | 3 | 258 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 128 | 129 | a | 0 | ... | | chr1 | 128 | 129 | a | 0 | ... | | chr1 | 128 | 129 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 64 | 65 | a | 0 | ... | | chr1 | 64 | 65 | a | 0 | ... | | chr1 | 64 | 65 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 256 | 257 | a | 0 | ... | | chr1 | 256 | 257 | a | 0 | ... | | chr1 | 256 | 257 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 192 | 193 | a | 0 | ... | | chr1 | 192 | 193 | a | 0 | ... | | chr1 | 192 | 193 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 232 | 233 | a | 0 | ... | | chr1 | 232 | 233 | a | 0 | ... | | chr1 | 232 | 233 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 252 | 253 | a | 0 | ... | | chr1 | 252 | 253 | a | 0 | ... | | chr1 | 252 | 253 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 257 | 258 | a | 0 | ... | | chr1 | 257 | 258 | a | 0 | ... | | chr1 | 257 | 258 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 2 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 129 | 130 | a | 0 | ... | | chr1 | 129 | 130 | a | 0 | ... | | chr1 | 129 | 130 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain154-method_chain154] __________ [gw8] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', False) method_chain = ('set_intersect', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('set_intersect', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:117 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E (and 127 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2AMz/T8byP0iIGBkQETAABTGwM7') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') __________ test_three_in_a_row[strandedness_chain141-method_chain141] __________ [gw3] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', 'opposite') method_chain = ('join', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('join', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:145 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 E (and 19 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') __________ test_three_in_a_row[strandedness_chain199-method_chain199] __________ [gw0] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', 'same') method_chain = ('set_union', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('set_union', 'nearest'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E (and 197 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2CAA0YGLAAAADUAAg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ___________ test_three_in_a_row[strandedness_chain89-method_chain89] ___________ [gw4] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', 'same'), method_chain = ('subtract', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('subtract', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:30 E /usr/lib/python3/dist-packages/pandas/core/dtypes/missing.py:207 E (and 19 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5852055 | 5856149 | a | 0 | + | | chr1 | 8479471 | 8485413 | a | 0 | - | | chr1 | 8987847 | 8995515 | a | 0 | - | | chr7 | 4669467 | 4672737 | a | 0 | - | | chr8 | 8174194 | 8174382 | a | 0 | - | | chr15 | 2044363 | 2046285 | a | 0 | - | | chr22 | 5534501 | 5538595 | a | 0 | + | | chrX | 2057500 | 2058624 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 8 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4313867 | 4314124 | a | 0 | - | | chr20 | 3117889 | 3117890 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4313867 | 4314124 | a | 0 | - | | chr20 | 3117889 | 3117890 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr11 | 1 | 258 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') __________ test_three_in_a_row[strandedness_chain180-method_chain180] __________ [gw1] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', False) method_chain = ('intersect', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('intersect', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:38 E (and 106 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') __________ test_three_in_a_row[strandedness_chain102-method_chain102] __________ [gw9] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', 'opposite') method_chain = ('set_union', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('set_union', 'intersect'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E (and 183 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2D0keZvMWHmZGBkwAIAIQoBPQ==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') __________ test_three_in_a_row[strandedness_chain190-method_chain190] __________ [gw6] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', False) method_chain = ('join', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('join', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:15 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:145 E (and 24 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BAAEYUCgwAAD4AAw==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') __________ test_three_in_a_row[strandedness_chain131-method_chain131] __________ [gw7] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', 'opposite') method_chain = ('intersect', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('intersect', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:30 E /usr/lib/python3/dist-packages/pandas/core/dtypes/missing.py:207 E (and 18 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAEECwEAAFEAAw==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ___________ test_three_in_a_row[strandedness_chain76-method_chain76] ___________ [gw5] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', 'same'), method_chain = ('nearest', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:63: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('nearest', 'join'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:53 E (and 29 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2TABIzYOHBBAACcAAU=') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain115-method_chain115] __________ [gw10] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', 'opposite'), method_chain = ('overlap', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('overlap', 'nearest'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | + | E | chr1 | 2 | 3 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E | chr1 | 1 | 5 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:53 E (and 29 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2QAAkbhzAoFBkZGRgZGMBdMQgAjjADJMTLCpGAqmBmReMjaAFt3AS0=') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4 | 261 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4 | 261 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4 | 261 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4 | 261 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4 | 261 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4 | 261 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4 | 261 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4 | 261 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4 | 261 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4 | 261 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4 | 261 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4 | 261 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4 | 12 | a | 0 | ... | | chr1 | 4 | 12 | a | 0 | ... | | chr1 | 4 | 12 | a | 0 | ... | | chr1 | 4 | 12 | a | 0 | ... | | chr1 | 4 | 12 | a | 0 | ... | | chr1 | 4 | 12 | a | 0 | ... | | chr1 | 4 | 12 | a | 0 | ... | | chr1 | 4 | 12 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 8 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain200-method_chain200] __________ [gw0] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', 'same') method_chain = ('set_union', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('set_union', 'intersect'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E (and 196 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2AMmqDPVcfAyMjIgAUAACvQAZ4=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') __________ test_three_in_a_row[strandedness_chain169-method_chain169] __________ [gw2] linux -- Python 3.12.6 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 880, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1722, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=('opposite', False), | method_chain=('nearest', 'set_intersect'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=Empty PyRanges, | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | (and 173 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2QAA0YGBGBEohihTLg8AADhAAg=') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3688, in set_intersect | other_clusters = other.merge(strand=strand) | ^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 381, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=('opposite', False), | method_chain=('nearest', 'set_intersect'), | gr=Empty PyRanges, | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:38 | (and 160 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAJGFApDCMJmBAAAywAI') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain155-method_chain155] __________ [gw8] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', False) method_chain = ('set_intersect', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('set_intersect', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:140 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E (and 106 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2CUSLwpV6Sgw8DAyIAJADmqAjE=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ___________ test_three_in_a_row[strandedness_chain90-method_chain90] ___________ [gw4] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', 'same'), method_chain = ('subtract', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('subtract', 'join'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:30 E (and 19 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +6 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 258 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 11 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 6 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b ('subtract', 'join') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +6 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 11 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 6 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b ('subtract', 'join') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +6 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 11 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 6 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +6 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr2 | 1 | 2 | a | 0 | ... | | chr2 | 1 | 2 | a | 0 | ... | | chr2 | 1 | 2 | a | 0 | ... | | chr2 | 1 | 2 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr2 | 1 | 2 | a | 0 | ... | | chr2 | 1 | 2 | a | 0 | ... | | chr2 | 1 | 2 | a | 0 | ... | | chr2 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 18 rows and 11 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 6 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b ('subtract', 'join') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +6 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr2 | 1 | 2 | a | 0 | ... | | chr2 | 1 | 2 | a | 0 | ... | | chr2 | 1 | 2 | a | 0 | ... | | chr2 | 1 | 2 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr2 | 1 | 2 | a | 0 | ... | | chr2 | 1 | 2 | a | 0 | ... | | chr2 | 1 | 2 | a | 0 | ... | | chr2 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 18 rows and 11 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 6 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b ('subtract', 'join') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +6 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr2 | 1 | 2 | a | 0 | ... | | chr2 | 1 | 2 | a | 0 | ... | | chr2 | 1 | 2 | a | 0 | ... | | chr2 | 1 | 2 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr2 | 1 | 2 | a | 0 | ... | | chr2 | 1 | 2 | a | 0 | ... | | chr2 | 1 | 2 | a | 0 | ... | | chr2 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 18 rows and 11 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 6 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') __________ test_three_in_a_row[strandedness_chain143-method_chain143] __________ [gw3] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', 'opposite'), method_chain = ('join', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:68: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2, suffix="_c") pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('join', 'nearest'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E | chr1 | 2 | 3 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 65537 | 65538 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:110 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E (and 30 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2SAAkYIwcgAoxlhooxQEk4wIuSRxUFicJVIkiAAAAWyABk=') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 2 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain209-method_chain209] __________ [gw5] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', 'same') method_chain = ('set_intersect', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('set_intersect', 'join'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 E /usr/lib/python3/dist-packages/pandas/core/array_algos/take.py:574 E (and 61 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2AUULffYCDry8jIgAUAAC1UAcQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') __________ test_three_in_a_row[strandedness_chain156-method_chain156] __________ [gw8] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', False) method_chain = ('set_intersect', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('set_intersect', 'overlap'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E (and 65 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2CUjWNW5+H7y8DIgAUAACthAb8=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') __________ test_three_in_a_row[strandedness_chain103-method_chain103] __________ [gw9] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', 'opposite') method_chain = ('set_union', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('set_union', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E /usr/lib/python3/dist-packages/natsort/utils.py:344 E (and 119 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2As6jsexCVgxMDAyIAJAEEMAmg=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') __________ test_three_in_a_row[strandedness_chain182-method_chain182] __________ [gw1] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', False) method_chain = ('subtract', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('subtract', 'set_union'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1048578 | 1048579 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=Empty PyRanges, E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:112 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:117 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 E (and 132 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY8vxyg9gYGBkYBcAEhAAoxkYACsBAZY=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain117-method_chain117] __________ [gw10] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', 'opposite') method_chain = ('overlap', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('overlap', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:145 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 E (and 27 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BAAEYUCgwAAD4AAw==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') __________ test_three_in_a_row[strandedness_chain201-method_chain201] __________ [gw0] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', 'same') method_chain = ('set_union', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('set_union', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E (and 134 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2D0ZtqwUk/4OwMDIwMmAABJOQLh') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') __________ test_three_in_a_row[strandedness_chain133-method_chain133] __________ [gw7] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', 'opposite') method_chain = ('subtract', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('subtract', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:112 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:117 E (and 139 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2AsYuPijRffxsDAyIAJACwMAb4=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') __________ test_three_in_a_row[strandedness_chain192-method_chain192] __________ [gw6] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', False), method_chain = ('join', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:68: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2, suffix="_c") pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:292: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('join', 'nearest'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 3 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:53 E (and 28 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2QAAUYwBDMgCMplgFEwGRQhIAAAAkwADg==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') Empty PyRanges ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain170-method_chain170] __________ [gw2] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', False), method_chain = ('nearest', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('nearest', 'overlap'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:53 E (and 29 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2RAAozYKAgTzgEAAM0ABw==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain157-method_chain157] __________ [gw8] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', False) method_chain = ('set_intersect', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('set_intersect', 'nearest'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 E /usr/lib/python3/dist-packages/pandas/core/array_algos/take.py:574 E /usr/lib/python3/dist-packages/pandas/core/common.py:143 E (and 62 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2CAA0YGLAAAADUAAg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') __________ test_three_in_a_row[strandedness_chain104-method_chain104] __________ [gw9] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', 'opposite'), method_chain = ('set_union', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('set_union', 'join'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E (and 182 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2B0Kj/FWyn+nIGRAQsAAE4qAwo=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ___________ test_three_in_a_row[strandedness_chain91-method_chain91] ___________ [gw4] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', 'same'), method_chain = ('join', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('join', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:17 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:21 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:37 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:43 E (and 40 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') __________ test_three_in_a_row[strandedness_chain210-method_chain210] __________ [gw5] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', 'same') method_chain = ('overlap', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('overlap', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:17 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:21 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:37 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:43 E (and 65 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') __________ test_three_in_a_row[strandedness_chain145-method_chain145] __________ [gw3] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', 'opposite'), method_chain = ('join', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('join', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 E /usr/lib/python3/dist-packages/pandas/core/array_algos/take.py:574 E (and 77 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') __________ test_three_in_a_row[strandedness_chain202-method_chain202] __________ [gw0] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', 'same'), method_chain = ('set_union', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('set_union', 'join'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E (and 197 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2CAA0YGLAAAADUAAg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') __________ test_three_in_a_row[strandedness_chain183-method_chain183] __________ [gw1] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', False) method_chain = ('subtract', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('subtract', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:112 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:117 E (and 117 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2DUDX0xy0FuAgMDIwMmAABM0gL1') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') __________ test_three_in_a_row[strandedness_chain158-method_chain158] __________ [gw8] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', False) method_chain = ('set_intersect', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('set_intersect', 'intersect'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E /usr/lib/python3/dist-packages/natsort/utils.py:344 E (and 67 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2DMZ/1iVcfACIRYAAA5dgIk') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') __________ test_three_in_a_row[strandedness_chain211-method_chain211] __________ [gw5] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', 'same') method_chain = ('overlap', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('overlap', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:145 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 E (and 27 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BAAEYGTAAAADQAAg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') __________ test_three_in_a_row[strandedness_chain194-method_chain194] __________ [gw6] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', False), method_chain = ('join', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('join', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:38 E (and 160 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') __________ test_three_in_a_row[strandedness_chain134-method_chain134] __________ [gw7] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', 'opposite') method_chain = ('subtract', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('subtract', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:112 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:117 E (and 118 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2A0jH2eoMtYxcDAyIAJAEGaAoA=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') __________ test_three_in_a_row[strandedness_chain105-method_chain105] __________ [gw9] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', 'opposite') method_chain = ('set_intersect', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('set_intersect', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E (and 128 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2Asas5WSOFfysjAyIAJAEQtApw=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') __________ test_three_in_a_row[strandedness_chain119-method_chain119] __________ [gw10] linux -- Python 3.12.6 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 880, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1722, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', 'opposite'), | method_chain=('nearest', 'set_union'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 65537 | 65794 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=Empty PyRanges, | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | (and 170 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2RkZAACIAlnAAkGMGCEMBgZ4CSQYAQAAhAAEQ==') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3784, in set_union | gr = gr.merge(strand=strand) | ^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 347, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', 'opposite'), | method_chain=('nearest', 'set_union'), | gr=Empty PyRanges, | gr2=Empty PyRanges, # or any other generated value | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/attr.py:65 | (and 259 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain184-method_chain184] __________ [gw1] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', False), method_chain = ('subtract', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('subtract', 'overlap'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:30 E /usr/lib/python3/dist-packages/pandas/core/dtypes/missing.py:207 E (and 18 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ___________ test_three_in_a_row[strandedness_chain92-method_chain92] ___________ [gw4] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', 'same'), method_chain = ('join', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('join', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 E /usr/lib/python3/dist-packages/pandas/core/array_algos/take.py:574 E (and 80 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') __________ test_three_in_a_row[strandedness_chain171-method_chain171] __________ [gw2] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', False), method_chain = ('nearest', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:63: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('nearest', 'nearest'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:73 E (and 27 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2QAA0YGBGCEkowoPAQAAAECAAg=') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain203-method_chain203] __________ [gw0] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', 'same') method_chain = ('set_intersect', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('set_intersect', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E (and 116 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2B09fOvrVfnY2BgZMAEADcCAhY=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') __________ test_three_in_a_row[strandedness_chain147-method_chain147] __________ [gw3] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', False) method_chain = ('set_union', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('set_union', 'set_union'), E gr=Empty PyRanges, # or any other generated value E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E (and 263 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BAAEYGTAAAADQAAg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') __________ test_three_in_a_row[strandedness_chain159-method_chain159] __________ [gw8] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', False) method_chain = ('set_intersect', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('set_intersect', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:140 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E (and 106 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2AMUzdenivOysjAyIAJADIAAeQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') __________ test_three_in_a_row[strandedness_chain135-method_chain135] __________ [gw7] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', 'opposite') method_chain = ('subtract', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('subtract', 'overlap'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:30 E /usr/lib/python3/dist-packages/pandas/core/dtypes/missing.py:207 E (and 18 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') __________ test_three_in_a_row[strandedness_chain196-method_chain196] __________ [gw6] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', 'same') method_chain = ('set_union', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('set_union', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E (and 255 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2DkKA7USVN2ZGRgZMAEAC37AcY=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') __________ test_three_in_a_row[strandedness_chain106-method_chain106] __________ [gw9] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', 'opposite') method_chain = ('set_intersect', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('set_intersect', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E /usr/lib/python3/dist-packages/natsort/utils.py:344 E (and 104 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2C0Epg0o4RxGwMDIwMmAABDPwKi') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') __________ test_three_in_a_row[strandedness_chain213-method_chain213] __________ [gw5] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', 'same'), method_chain = ('overlap', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('overlap', 'nearest'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 257 | 258 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:53 E (and 29 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2QAA0YGBGBkRBdiRJGG0gABRQAJ') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 2 | 9 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 2 | 9 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 7 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 7 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 258 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain160-method_chain160] __________ [gw8] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', False) method_chain = ('set_intersect', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('set_intersect', 'join'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 E /usr/lib/python3/dist-packages/pandas/core/array_algos/take.py:574 E (and 61 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkVHBcKSLZwMDIgAUAACvAAbs=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') __________ test_three_in_a_row[strandedness_chain204-method_chain204] __________ [gw0] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', 'same') method_chain = ('set_intersect', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('set_intersect', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E /usr/lib/python3/dist-packages/natsort/utils.py:344 E (and 104 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2DUn7LEtFadn4GBkQETAAA9uAJS') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') __________ test_three_in_a_row[strandedness_chain185-method_chain185] __________ [gw1] linux -- Python 3.12.6 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 880, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1722, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 292, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=('opposite', False), | method_chain=('subtract', 'nearest'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=Empty PyRanges, | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:53 | (and 29 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2QAA0YGJMCIymCE02AAAADlAAg=') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 4384, in subtract | other_clusters = other.merge(strand=strand) | ^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 347, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=('opposite', False), | method_chain=('subtract', 'nearest'), | gr=Empty PyRanges, | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=Empty PyRanges, # or any other generated value | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:143 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:30 | (and 19 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain148-method_chain148] __________ [gw3] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', False) method_chain = ('set_union', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('set_union', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/init.py:174 E (and 205 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2Dksfwga6s2hZGBkQETAAA7EgJN') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') __________ test_three_in_a_row[strandedness_chain120-method_chain120] __________ [gw10] linux -- Python 3.12.6 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 880, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1722, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', 'opposite'), | method_chain=('nearest', 'set_intersect'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=Empty PyRanges, | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | (and 194 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2QAA0YGOGBkRBJihDLh8gAA/wAJ') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3688, in set_intersect | other_clusters = other.merge(strand=strand) | ^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 347, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', 'opposite'), | method_chain=('nearest', 'set_intersect'), | gr=Empty PyRanges, | gr2=Empty PyRanges, | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 257 | 258 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 | /usr/lib/python3/dist-packages/pandas/core/array_algos/take.py:574 | (and 84 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BAAEYkEkEDAABQAAQ=') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty 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Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain219-method_chain219] __________ [gw4] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', 'same'), method_chain = ('nearest', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('nearest', 'overlap'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:73 E (and 27 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2QAA0YGOGBkRBKCicPlAQD0AAg=') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain172-method_chain172] __________ [gw2] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', False) method_chain = ('nearest', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('nearest', 'intersect'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:53 E (and 29 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2RAAowQkhGZx4DGAQAA4AAH') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain107-method_chain107] __________ [gw9] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', 'opposite') method_chain = ('set_intersect', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('set_intersect', 'overlap'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E (and 65 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2C0Mf5fzsyYw8DIgAUAAD3EAlg=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') __________ test_three_in_a_row[strandedness_chain197-method_chain197] __________ [gw6] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', 'same') method_chain = ('set_union', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('set_union', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E (and 134 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2DkUcw6UCHCyMAARBgAADGmAec=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') __________ test_three_in_a_row[strandedness_chain136-method_chain136] __________ [gw7] linux -- Python 3.12.6 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 880, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1722, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', 'opposite'), | method_chain=('subtract', 'nearest'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=Empty PyRanges, | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:53 | (and 29 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2QAA0YGrIARiYKwGQEAswAH') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 4384, in subtract | other_clusters = other.merge(strand=strand) | ^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 347, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', 'opposite'), | method_chain=('subtract', 'nearest'), | gr=Empty PyRanges, | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=Empty PyRanges, # or any other generated value | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:143 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:30 | (and 19 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2CAA0YUCgIAAEAAAw==') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain149-method_chain149] __________ [gw3] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', False) method_chain = ('set_union', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('set_union', 'overlap'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E (and 192 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2CAA0YGLAAAADUAAg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') __________ test_three_in_a_row[strandedness_chain205-method_chain205] __________ [gw0] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', 'same') method_chain = ('set_intersect', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('set_intersect', 'overlap'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E (and 65 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2AMlT/K7sq4g4GRAQsAADoxAkE=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') __________ test_three_in_a_row[strandedness_chain161-method_chain161] __________ [gw8] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', False) method_chain = ('overlap', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('overlap', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:33 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:41 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:17 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:21 E (and 141 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') __________ test_three_in_a_row[strandedness_chain186-method_chain186] __________ [gw1] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', False) method_chain = ('subtract', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('subtract', 'intersect'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:30 E /usr/lib/python3/dist-packages/pandas/core/dtypes/missing.py:207 E (and 18 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') __________ test_three_in_a_row[strandedness_chain215-method_chain215] __________ [gw5] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', 'same') method_chain = ('overlap', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('overlap', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:30 E /usr/lib/python3/dist-packages/pandas/core/dtypes/missing.py:207 E (and 18 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 265 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 3781 | a | 0 | + | | chr1 | 1 | 265 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('overlap', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 3781 | a | 0 | + | | chr1 | 1 | 265 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('overlap', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 3781 | a | 0 | + | | chr1 | 1 | 265 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 3781 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('overlap', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 3781 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('overlap', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 3781 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') __________ test_three_in_a_row[strandedness_chain247-method_chain247] __________ [gw9] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', 'opposite') method_chain = ('set_union', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('set_union', 'overlap'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E (and 196 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2CsZmBgyGd5x8DIgAUAAC7aAd8=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') __________ test_three_in_a_row[strandedness_chain238-method_chain238] __________ [gw6] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', 'same'), method_chain = ('join', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('join', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:17 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:21 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:37 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:43 E (and 39 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAEECwEAAFEAAw==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') __________ test_three_in_a_row[strandedness_chain206-method_chain206] __________ [gw0] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', 'same') method_chain = ('set_intersect', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('set_intersect', 'nearest'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 E /usr/lib/python3/dist-packages/pandas/core/array_algos/take.py:574 E (and 61 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2CAA0YGLAAAADUAAg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') __________ test_three_in_a_row[strandedness_chain121-method_chain121] __________ [gw10] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', 'opposite'), method_chain = ('nearest', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('nearest', 'overlap'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:53 E (and 28 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2RAAozYKChHXYJdulS1hxEABq8Bjg==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain220-method_chain220] __________ [gw4] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', 'same'), method_chain = ('nearest', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:63: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('nearest', 'nearest'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:53 E (and 30 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2TABIxIFCOUyQiTBAAAugAH') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain162-method_chain162] __________ [gw8] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', False) method_chain = ('overlap', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('overlap', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:38 E (and 106 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') __________ test_three_in_a_row[strandedness_chain229-method_chain229] __________ [gw7] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', 'same') method_chain = ('intersect', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('intersect', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:145 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 E /usr/lib/python3/dist-packages/pandas/core/dtypes/missing.py:207 E (and 18 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') __________ test_three_in_a_row[strandedness_chain264-method_chain264] __________ [gw3] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', 'opposite') method_chain = ('overlap', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('overlap', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:145 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 E (and 27 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BAAEYUCgwAAD4AAw==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') __________ test_three_in_a_row[strandedness_chain173-method_chain173] __________ [gw2] linux -- Python 3.12.6 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 880, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1722, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=('opposite', False), | method_chain=('nearest', 'subtract'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=Empty PyRanges, | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:110 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 | (and 28 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2QAA0YGOGBEYqNIQAEAAOAABg==') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 4384, in subtract | other_clusters = other.merge(strand=strand) | ^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 381, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=('opposite', False), | method_chain=('nearest', 'subtract'), | gr=Empty PyRanges, | gr2=Empty PyRanges, | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:369 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:373 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:378 | (and 24 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkAAJGEGIEM6FcKAEAAKIACA==') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 5921 | a | 0 | ... | | chr1 | 1 | 5921 | a | 0 | ... | | chr1 | 1 | 5921 | a | 0 | ... | | chr1 | 1 | 5921 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 258 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 258 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain248-method_chain248] __________ [gw9] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', 'opposite') method_chain = ('set_union', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('set_union', 'nearest'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E (and 197 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2CAA0YGLAAAADUAAg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') __________ test_three_in_a_row[strandedness_chain255-method_chain255] __________ [gw1] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', 'opposite') method_chain = ('set_intersect', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('set_intersect', 'nearest'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 E /usr/lib/python3/dist-packages/pandas/core/array_algos/take.py:574 E (and 61 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkjXrgnSB7hZGRAQsAAEkzAt8=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') __________ test_three_in_a_row[strandedness_chain239-method_chain239] __________ [gw6] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', 'same') method_chain = ('join', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('join', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 E /usr/lib/python3/dist-packages/pandas/core/array_algos/take.py:574 E (and 77 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') __________ test_three_in_a_row[strandedness_chain207-method_chain207] __________ [gw0] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', 'same') method_chain = ('set_intersect', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('set_intersect', 'intersect'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E /usr/lib/python3/dist-packages/natsort/utils.py:344 E (and 66 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2DMiFe2rWJgYGBkwAIALEsBpA==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') __________ test_three_in_a_row[strandedness_chain256-method_chain256] __________ [gw1] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', 'opposite') method_chain = ('set_intersect', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('set_intersect', 'intersect'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E /usr/lib/python3/dist-packages/natsort/utils.py:344 E (and 66 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2CAA0YGLAAAADUAAg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') __________ test_three_in_a_row[strandedness_chain249-method_chain249] __________ [gw9] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', 'opposite') method_chain = ('set_union', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('set_union', 'intersect'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E (and 196 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2CAA0YGLAAAADUAAg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') __________ test_three_in_a_row[strandedness_chain217-method_chain217] __________ [gw5] linux -- Python 3.12.6 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 880, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1722, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=('opposite', 'same'), | method_chain=('nearest', 'set_union'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=Empty PyRanges, | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | (and 170 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2TABIxQkhELDwgAANoACA==') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3784, in set_union | gr = gr.merge(strand=strand) | ^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 347, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=('opposite', 'same'), | method_chain=('nearest', 'set_union'), | gr=Empty PyRanges, | gr2=Empty PyRanges, | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 | (and 216 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAEECwEAAFEAAw==') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain174-method_chain174] __________ [gw2] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', False), method_chain = ('nearest', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:63: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('nearest', 'join'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:53 E (and 30 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2QAA0YGBGBEohihTLg8AADhAAg=') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') __________ test_three_in_a_row[strandedness_chain231-method_chain231] __________ [gw7] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', 'same') method_chain = ('subtract', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('subtract', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:112 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:117 E (and 129 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BMSrEOt2e8ysDAyIAJAD7MAnA=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') __________ test_three_in_a_row[strandedness_chain221-method_chain221] __________ [gw4] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', 'same') method_chain = ('nearest', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('nearest', 'intersect'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:73 E (and 27 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2RAB4xgCGXCCBQAAADxAAc=') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain122-method_chain122] __________ [gw10] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', 'opposite'), method_chain = ('nearest', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:63: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('nearest', 'nearest'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:73 E (and 27 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2TABIzYOIwsOq3uWmpLGAEI1AH2') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain271-method_chain271] __________ [gw8] linux -- Python 3.12.6 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 880, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1722, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=('opposite', 'opposite'), | method_chain=('nearest', 'subtract'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr2 | 13 | 14 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr2 | 65537 | 74763 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=Empty PyRanges, | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:110 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 | (and 28 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY+RiYPBnYGBgBGIGHgjFyMgIEQEhEFNbhRPIhokyAAAZIgDM') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 4384, in subtract | other_clusters = other.merge(strand=strand) | ^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 347, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=('opposite', 'opposite'), | method_chain=('nearest', 'subtract'), | gr=Empty PyRanges, | gr2=Empty PyRanges, # or any other generated value | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:143 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:30 | (and 19 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 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('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr2 | 13 | 14 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr2 | 13 | 14 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr2 | 13 | 14 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain250-method_chain250] __________ [gw9] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', 'opposite') method_chain = ('set_union', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('set_union', 'subtract'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E (and 246 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') __________ test_three_in_a_row[strandedness_chain266-method_chain266] __________ [gw3] linux -- Python 3.12.6 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 880, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1722, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=('opposite', 'opposite'), | method_chain=('nearest', 'set_union'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 65537 | 65538 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=Empty PyRanges, | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | (and 170 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2RkYGBgBBEQCsyCiClXz2Bm1PXlOAfkM4IkmcBSjDDVCBJEAABtmQKi') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3784, in set_union | gr = gr.merge(strand=strand) | ^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 347, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=('opposite', 'opposite'), | method_chain=('nearest', 'set_union'), | gr=Empty PyRanges, | gr2=Empty PyRanges, # or any other generated value | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/attr.py:65 | (and 257 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain208-method_chain208] __________ [gw0] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', 'same') method_chain = ('set_intersect', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('set_intersect', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E (and 103 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2DkTO48w8Rkw8DAyIAJADUbAgQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') __________ test_three_in_a_row[strandedness_chain257-method_chain257] __________ [gw1] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', 'opposite') method_chain = ('set_intersect', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('set_intersect', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E (and 103 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2C0yFr/0VpciZGBkQETAABIPwK6') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') __________ test_three_in_a_row[strandedness_chain285-method_chain285] __________ [gw2] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', 'opposite') method_chain = ('subtract', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('subtract', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:30 E (and 19 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAEECwEAAFEAAw==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4444208 | 4444209 | a | 0 | + | | chr1 | 1103 | 6311 | a | 0 | + | | chr1 | 1337 | 1594 | a | 0 | - | | chr1 | 875 | 1132 | a | 0 | - | | chr1 | 593 | 850 | a | 0 | - | | chr1 | 1337 | 1348 | a | 0 | - | | chr1 | 1337 | 1348 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 7 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr2 | 4444208 | 4445083 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr2 | 65537 | 65794 | a | 0 | - | | chr2 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 258 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr2 | 65537 | 65794 | a | 0 | - | | chr2 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr2 | 65537 | 65794 | a | 0 | - | | chr2 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr10 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') __________ test_three_in_a_row[strandedness_chain241-method_chain241] __________ [gw6] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', 'same'), method_chain = ('join', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:68: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2, suffix="_c") pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('join', 'nearest'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:73 E (and 27 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2QAA0YGOGBkxBCCshnBECHFCAABdQAM') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 258 | a | 0 | ... | | chr1 | 1 | 258 | a | 0 | ... | | chr1 | 1 | 258 | a | 0 | ... | | chr1 | 1 | 258 | a | 0 | ... | | chr1 | 1 | 258 | a | 0 | ... | | chr1 | 1 | 258 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 1 | 258 | a | 0 | ... | | chr1 | 1 | 258 | a | 0 | ... | | chr1 | 1 | 258 | a | 0 | ... | | chr1 | 1 | 258 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 258 | a | 0 | ... | | chr1 | 1 | 258 | a | 0 | ... | | chr1 | 1 | 258 | a | 0 | ... | | chr1 | 1 | 258 | a | 0 | ... | | chr1 | 1 | 258 | a | 0 | ... | | chr1 | 1 | 258 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain278-method_chain278] __________ [gw10] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', 'opposite') method_chain = ('intersect', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('intersect', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:145 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 E (and 27 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') __________ test_three_in_a_row[strandedness_chain251-method_chain251] __________ [gw9] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', 'opposite') method_chain = ('set_union', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('set_union', 'join'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E (and 197 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2Bkc2VfwiXizsjIgAUAACNCAV8=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') __________ test_three_in_a_row[strandedness_chain218-method_chain218] __________ [gw5] linux -- Python 3.12.6 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 880, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1722, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=('opposite', 'same'), | method_chain=('nearest', 'set_intersect'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr2 | 2 | 3 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr2 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=Empty PyRanges, | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | (and 173 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2QAAUYQYoSwGBlgNCNCDjsAAAILAAw=') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3688, in set_intersect | other_clusters = other.merge(strand=strand) | ^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 347, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=('opposite', 'same'), | method_chain=('nearest', 'set_intersect'), | gr=Empty PyRanges, | gr2=Empty PyRanges, | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 | /usr/lib/python3/dist-packages/pandas/core/array_algos/take.py:574 | (and 77 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2A0KphflSQXzMjAyAAGUAoMAEDLApM=') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain292-method_chain292] __________ [gw0] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', 'opposite') method_chain = ('join', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('join', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:30 E (and 19 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BAAEYUCgwAAD4AAw==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +6 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5054586 | 5059718 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 11 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 6 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b ('join', 'subtract') Empty PyRanges ('join', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +6 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5054586 | 5059718 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 11 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 6 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b ('join', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +6 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5054586 | 5059718 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 11 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 6 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') __________ test_three_in_a_row[strandedness_chain232-method_chain232] __________ [gw7] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', 'same') method_chain = ('subtract', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('subtract', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:112 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:117 E (and 116 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BUVQg2ZWbey8DAyIAJACezAZM=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') __________ test_three_in_a_row[strandedness_chain258-method_chain258] __________ [gw1] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', 'opposite') method_chain = ('set_intersect', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('set_intersect', 'join'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 E /usr/lib/python3/dist-packages/pandas/core/array_algos/take.py:574 E /usr/lib/python3/dist-packages/pandas/core/common.py:143 E (and 62 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2CAA0YGLAAAADUAAg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges 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('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') __________ test_three_in_a_row[strandedness_chain222-method_chain222] __________ [gw4] linux -- Python 3.12.6 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 880, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1722, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=('opposite', 'same'), | method_chain=('nearest', 'subtract'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=Empty PyRanges, | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:73 | (and 27 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2QAA0YGOGBkRBJCEocCAADyAAc=') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 4384, in subtract | other_clusters = other.merge(strand=strand) | ^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 347, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=('opposite', 'same'), | method_chain=('nearest', 'subtract'), | gr=Empty PyRanges, | gr2=Empty PyRanges, | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 4 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:143 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:30 | (and 19 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BAAEYkihGMGQEASQAG') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 258 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain272-method_chain272] __________ [gw8] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', 'opposite') method_chain = ('nearest', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:63: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('nearest', 'join'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:73 E (and 26 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2RAAowQkpEBLwAAAMsABQ==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain298-method_chain298] __________ [gw5] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = (False, None), method_chain = ('set_union', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('set_union', 'intersect'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:33 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E (and 240 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2CAA0YGLAAAADUAAg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') __________ test_three_in_a_row[strandedness_chain243-method_chain243] __________ [gw6] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', 'same'), method_chain = ('join', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('join', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:145 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 E (and 19 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') __________ test_three_in_a_row[strandedness_chain267-method_chain267] __________ [gw3] linux -- Python 3.12.6 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 880, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1722, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=('opposite', 'opposite'), | method_chain=('nearest', 'set_intersect'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=Empty PyRanges, | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | (and 173 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2QAA0YGBICyGRmROQgVAAEDAAk=') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3688, in set_intersect | other_clusters = other.merge(strand=strand) | ^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 347, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=('opposite', 'opposite'), | method_chain=('nearest', 'set_intersect'), | gr=Empty PyRanges, | gr2=Empty PyRanges, # or any other generated value | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 | /usr/lib/python3/dist-packages/pandas/core/array_algos/take.py:574 | (and 77 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BAAEYUCgwAAD4AAw==') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain286-method_chain286] __________ [gw2] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', 'opposite') method_chain = ('subtract', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('subtract', 'join'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:30 E (and 19 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +6 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 9132820 | 9142512 | a | 0 | ... | | chr3 | 9668108 | 9676320 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 11 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 6 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +6 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 258 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 11 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 6 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +6 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 258 | a | 0 | ... | | chr1 | 1 | 258 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 11 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 6 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +6 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 11 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 6 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +6 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 11 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 6 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +6 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 11 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 6 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +6 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 258 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 11 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 6 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') __________ test_three_in_a_row[strandedness_chain233-method_chain233] __________ [gw7] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', 'same') method_chain = ('subtract', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('subtract', 'overlap'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:30 E /usr/lib/python3/dist-packages/pandas/core/dtypes/missing.py:207 E (and 18 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') __________ test_three_in_a_row[strandedness_chain252-method_chain252] __________ [gw9] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', 'opposite') method_chain = ('set_intersect', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('set_intersect', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E (and 133 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2C0a/Vzy+Y6wcDAyIAJAEKUApc=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') __________ test_three_in_a_row[strandedness_chain259-method_chain259] __________ [gw1] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', 'opposite') method_chain = ('overlap', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('overlap', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/attr.py:65 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:17 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:21 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:37 E (and 89 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') __________ test_three_in_a_row[strandedness_chain280-method_chain280] __________ [gw10] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', 'opposite') method_chain = ('subtract', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('subtract', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:112 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:117 E (and 137 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2DUL3n+jlXAnoGBkQETAABKgwLP') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') __________ test_three_in_a_row[strandedness_chain294-method_chain294] __________ [gw0] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = (False, None), method_chain = ('set_union', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('set_union', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:33 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E (and 282 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2D0CFwRa8lwn4GBkQETAABGGQK5') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') __________ test_three_in_a_row[strandedness_chain273-method_chain273] __________ [gw8] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', 'opposite') method_chain = ('intersect', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('intersect', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/attr.py:11 E (and 333 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') __________ test_three_in_a_row[strandedness_chain299-method_chain299] __________ [gw5] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = (False, None), method_chain = ('set_union', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('set_union', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:38 E (and 202 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2CU8qx/768SzMjAyIAJAEOMAps=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') __________ test_three_in_a_row[strandedness_chain223-method_chain223] __________ [gw4] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', 'same'), method_chain = ('nearest', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:63: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('nearest', 'join'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:73 E (and 27 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2QAA0YGOGBkRBKCicPlAQD0AAg=') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain245-method_chain245] __________ [gw6] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', 'opposite') method_chain = ('set_union', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('set_union', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E (and 253 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2C0Sm3iTGY4zsjAyIAJADwxAlg=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') __________ test_three_in_a_row[strandedness_chain260-method_chain260] __________ [gw1] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', 'opposite') method_chain = ('overlap', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('overlap', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:145 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 E /usr/lib/python3/dist-packages/pandas/core/dtypes/missing.py:207 E (and 18 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BAAEYUCgwAAD4AAw==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') __________ test_three_in_a_row[strandedness_chain287-method_chain287] __________ [gw2] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', 'opposite') method_chain = ('join', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('join', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/attr.py:65 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:17 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:21 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:37 E (and 64 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') __________ test_three_in_a_row[strandedness_chain253-method_chain253] __________ [gw9] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', 'opposite') method_chain = ('set_intersect', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('set_intersect', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E (and 103 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2D0skw+mMPOwcDAyIAJADjmAiU=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') __________ test_three_in_a_row[strandedness_chain268-method_chain268] __________ [gw3] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', 'opposite') method_chain = ('nearest', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('nearest', 'overlap'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:73 E (and 27 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2RAAowQkpEBLwAAAMsABQ==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain274-method_chain274] __________ [gw8] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', 'opposite') method_chain = ('intersect', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('intersect', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:145 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 E (and 27 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') __________ test_three_in_a_row[strandedness_chain295-method_chain295] __________ [gw0] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = (False, None) method_chain = ('set_union', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('set_union', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:38 E (and 200 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BU1lBLSeLbzMDAyIAJADHJAfs=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') __________ test_three_in_a_row[strandedness_chain281-method_chain281] __________ [gw10] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', 'opposite') method_chain = ('subtract', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('subtract', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:112 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:117 E (and 116 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2C0lb7BlibdyMDAyIAJADmnAjs=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') __________ test_three_in_a_row[strandedness_chain234-method_chain234] __________ [gw7] linux -- Python 3.12.6 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 880, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1722, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=('opposite', 'same'), | method_chain=('subtract', 'nearest'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 4716 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=Empty PyRanges, | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:53 | (and 29 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2QAAUYwhDIYhDIZYHyIGDIFZgIAEYkAhw==') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 4384, in subtract | other_clusters = other.merge(strand=strand) | ^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 347, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=('opposite', 'same'), | method_chain=('subtract', 'nearest'), | gr=Empty PyRanges, | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=Empty PyRanges, # or any other generated value | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:143 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:30 | (and 19 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2CAA0YUCgIAAEAAAw==') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 4715 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 4715 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 4715 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain300-method_chain300] __________ [gw5] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = (False, None), method_chain = ('set_union', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('set_union', 'join'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:33 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E (and 246 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2CAA0YGLAAAADUAAg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') __________ test_three_in_a_row[strandedness_chain254-method_chain254] __________ [gw9] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', 'opposite') method_chain = ('set_intersect', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('set_intersect', 'overlap'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E /usr/lib/python3/dist-packages/natsort/utils.py:344 E (and 66 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2CAA0YGLAAAADUAAg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') __________ test_three_in_a_row[strandedness_chain296-method_chain296] __________ [gw0] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = (False, None), method_chain = ('set_union', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('set_union', 'overlap'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:33 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E (and 239 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2CAA0YGLAAAADUAAg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') __________ test_three_in_a_row[strandedness_chain224-method_chain224] __________ [gw4] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', 'same') method_chain = ('intersect', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('intersect', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E (and 150 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') __________ test_three_in_a_row[strandedness_chain246-method_chain246] __________ [gw6] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', 'opposite') method_chain = ('set_union', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('set_union', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E (and 135 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BUCNQ/Wc3AwAiEmAAAMkUB6A==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') __________ test_three_in_a_row[strandedness_chain288-method_chain288] __________ [gw2] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', 'opposite') method_chain = ('join', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('join', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 E /usr/lib/python3/dist-packages/pandas/core/array_algos/take.py:574 E (and 61 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') __________ test_three_in_a_row[strandedness_chain282-method_chain282] __________ [gw10] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', 'opposite') method_chain = ('subtract', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('subtract', 'overlap'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:30 E /usr/lib/python3/dist-packages/pandas/core/dtypes/missing.py:207 E /usr/lib/python3/dist-packages/pandas/core/dtypes/missing.py:293 E (and 18 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') __________ test_three_in_a_row[strandedness_chain235-method_chain235] __________ [gw7] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', 'same') method_chain = ('subtract', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('subtract', 'intersect'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:30 E /usr/lib/python3/dist-packages/pandas/core/dtypes/missing.py:207 E (and 18 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2CAA0YUCgIAAEAAAw==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') __________ test_three_in_a_row[strandedness_chain297-method_chain297] __________ [gw0] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = (False, None), method_chain = ('set_union', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('set_union', 'nearest'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:33 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E (and 246 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2CAA0YGLAAAADUAAg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') __________ test_three_in_a_row[strandedness_chain301-method_chain301] __________ [gw5] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = (False, None) method_chain = ('set_intersect', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('set_intersect', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:38 E (and 200 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2B0Y/5gF8+pzcDAyIAJADYrAg0=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') __________ test_three_in_a_row[strandedness_chain269-method_chain269] __________ [gw3] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', 'opposite') method_chain = ('nearest', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:63: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('nearest', 'nearest'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:73 E (and 27 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2QAA0YGGGAEQ4QgTIaRu8+7nldiGiMACzwCKA==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') __________ test_three_in_a_row[strandedness_chain225-method_chain225] __________ [gw4] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', 'same') method_chain = ('intersect', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('intersect', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:145 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 E /usr/lib/python3/dist-packages/pandas/core/dtypes/missing.py:207 E (and 18 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') __________ test_three_in_a_row[strandedness_chain262-method_chain262] __________ [gw1] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', 'opposite') method_chain = ('overlap', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('overlap', 'nearest'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E | chr1 | 2 | 3 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:53 E (and 29 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2QAAkYIZmSEcSCAESwIZaPIMaJQYAAAAsEADw==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 128 | 129 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 64 | 65 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 256 | 257 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 192 | 193 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 232 | 233 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 252 | 253 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 257 | 258 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 129 | 130 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain304-method_chain304] __________ [gw6] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = (False, None), method_chain = ('set_intersect', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('set_intersect', 'nearest'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:38 E (and 138 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2DkYPoVWq/Ox8DIgAUAADXDAhA=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') __________ test_three_in_a_row[strandedness_chain276-method_chain276] __________ [gw8] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', 'opposite') method_chain = ('intersect', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('intersect', 'nearest'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 3 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:53 E (and 29 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2QAA0YGBjgDzoZLMIIhqkIgEwABagAL') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5 | 11 | a | 0 | ... | | chr1 | 4 | 13 | a | 0 | ... | | chr1 | 4 | 13 | a | 0 | ... | | chr1 | 4 | 13 | a | 0 | ... | | chr1 | 4 | 5 | a | 0 | ... | | chr1 | 4 | 13 | a | 0 | ... | | chr1 | 4 | 13 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 7 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 9 | 10 | a | 0 | ... | | chr1 | 9 | 10 | a | 0 | ... | | chr1 | 9 | 10 | a | 0 | ... | | chr1 | 9 | 10 | a | 0 | ... | | chr1 | 9 | 10 | a | 0 | ... | | chr1 | 9 | 10 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5 | 11 | a | 0 | ... | | chr1 | 4 | 5 | a | 0 | ... | | chr1 | 4 | 5 | a | 0 | ... | | chr1 | 4 | 5 | a | 0 | ... | | chr1 | 4 | 5 | a | 0 | ... | | chr1 | 4 | 5 | a | 0 | ... | | chr1 | 4 | 5 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 7 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5 | 11 | a | 0 | ... | | chr1 | 4 | 13 | a | 0 | ... | | chr1 | 4 | 13 | a | 0 | ... | | chr1 | 4 | 13 | a | 0 | ... | | chr1 | 4 | 5 | a | 0 | ... | | chr1 | 4 | 13 | a | 0 | ... | | chr1 | 4 | 13 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 7 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 6 | 7 | a | 0 | ... | | chr1 | 6 | 7 | a | 0 | ... | | chr1 | 6 | 7 | a | 0 | ... | | chr1 | 6 | 7 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 6 | 7 | a | 0 | ... | | chr1 | 6 | 7 | a | 0 | ... | | chr1 | 6 | 7 | a | 0 | ... | | chr1 | 6 | 7 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 9 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 6 | 7 | a | 0 | ... | | chr1 | 6 | 7 | a | 0 | ... | | chr1 | 6 | 7 | a | 0 | ... | | chr1 | 6 | 7 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 6 | 7 | a | 0 | ... | | chr1 | 6 | 7 | a | 0 | ... | | chr1 | 6 | 7 | a | 0 | ... | | chr1 | 6 | 7 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 9 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 6 | 7 | a | 0 | ... | | chr1 | 6 | 7 | a | 0 | ... | | chr1 | 6 | 7 | a | 0 | ... | | chr1 | 6 | 7 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 6 | 7 | a | 0 | ... | | chr1 | 6 | 7 | a | 0 | ... | | chr1 | 6 | 7 | a | 0 | ... | | chr1 | 6 | 7 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 9 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 6 | 7 | a | 0 | ... | | chr1 | 6 | 7 | a | 0 | ... | | chr1 | 6 | 7 | a | 0 | ... | | chr1 | 6 | 7 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 6 | 7 | a | 0 | ... | | chr1 | 6 | 7 | a | 0 | ... | | chr1 | 6 | 7 | a | 0 | ... | | chr1 | 6 | 7 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 9 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 9 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 9 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 6 | 7 | a | 0 | ... | | chr1 | 6 | 7 | a | 0 | ... | | chr1 | 6 | 7 | a | 0 | ... | | chr1 | 6 | 7 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 6 | 7 | a | 0 | ... | | chr1 | 6 | 7 | a | 0 | ... | | chr1 | 6 | 7 | a | 0 | ... | | chr1 | 6 | 7 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 10 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 10 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 10 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 6 | 15 | a | 0 | ... | | chr1 | 6 | 15 | a | 0 | ... | | chr1 | 6 | 15 | a | 0 | ... | | chr1 | 6 | 15 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 6 | 15 | a | 0 | ... | | chr1 | 6 | 15 | a | 0 | ... | | chr1 | 6 | 15 | a | 0 | ... | | chr1 | 6 | 15 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 10 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 257 | 258 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 257 | 258 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 257 | 258 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 6 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain305-method_chain305] __________ [gw6] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = (False, None) method_chain = ('set_intersect', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('set_intersect', 'intersect'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 E (and 138 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2AUZ5fnVeRaw8jIgAUAABv7ASU=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') __________ test_three_in_a_row[strandedness_chain236-method_chain236] __________ [gw7] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', 'same') method_chain = ('subtract', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('subtract', 'subtract'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:30 E (and 19 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | | chr2 | 1 | 2 | a | 0 | - | | chr2 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | | chr2 | 1 | 2 | a | 0 | - | | chr2 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | | chr2 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | | chr2 | 1 | 2 | a | 0 | - | | chr2 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | | chr2 | 1 | 2 | a | 0 | - | | chr2 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 124 | a | 0 | - | | chr1 | 1 | 124 | a | 0 | - | | chr2 | 1 | 124 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 124 | a | 0 | - | | chr1 | 1 | 124 | a | 0 | - | | chr2 | 1 | 124 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 124 | a | 0 | - | | chr1 | 1 | 124 | a | 0 | - | | chr2 | 1 | 124 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr2 | 1 | 3 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr2 | 1 | 3 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr2 | 1 | 3 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 65537 | 65538 | a | 0 | + | | chr1 | 65537 | 65538 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') __________ test_three_in_a_row[strandedness_chain311-method_chain311] __________ [gw9] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = (False, None), method_chain = ('overlap', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:292: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('overlap', 'nearest'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 3 | 4 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 3 | 4 | a | 0 | + | E | chr1 | 1 | 2 | a | 0 | + | E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:73 E (and 27 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2RkAAJGIAQhJjADzGW0qXlrweiUsHsWY1RjXhQDRB0jAw9IFSNUFwQgc2BiIAAATbIFng==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 65538 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 6668735 | 6671358 | a | 0 | ... | | chr1 | 4890125 | 4895182 | a | 0 | ... | | chr1 | 1783271 | 1792753 | a | 0 | ... | | chr11 | 5391519 | 5401001 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr15 | 3983816 | 3993298 | a | 0 | ... | | chr16 | 6610752 | 6617748 | a | 0 | ... | | chr21 | 8354463 | 8361463 | a | 0 | ... | | chrM | 4756721 | 4761630 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 9 rows and 12 columns from 7 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 6 | 5639 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 4912 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 2626 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 2626 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 2626 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 2626 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 2626 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 2626 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 2626 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 2626 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 2626 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 2626 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 2626 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 8 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain302-method_chain302] __________ [gw5] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = (False, None) method_chain = ('set_intersect', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('set_intersect', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 E (and 175 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2AUYTSKLlfiY2RgZMAEACFcAU0=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') __________ test_three_in_a_row[strandedness_chain331-method_chain331] __________ [gw8] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = (False, None), method_chain = ('subtract', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('subtract', 'overlap'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:38 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:369 E (and 23 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') __________ test_three_in_a_row[strandedness_chain321-method_chain321] __________ [gw0] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = (False, None), method_chain = ('nearest', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:63: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:292: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('nearest', 'join'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:73 E (and 28 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2RAAozYKChHZJrTDC8VJkYAC5kB+w==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') __________ test_three_in_a_row[strandedness_chain290-method_chain290] __________ [gw2] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', 'opposite') method_chain = ('join', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:68: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2, suffix="_c") pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('join', 'nearest'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:53 E (and 29 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2QAA0YGOGBkhPCRhGBsRiQ2AAFYAAo=') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 5 | a | 0 | ... | | chr1 | 1 | 5 | a | 0 | ... | | chr1 | 1 | 5 | a | 0 | ... | | chr1 | 1 | 5 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr2 | 1 | 5 | a | 0 | ... | | chr2 | 1 | 5 | a | 0 | ... | | chr2 | 1 | 258 | a | 0 | ... | | chr2 | 1 | 5 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 12 rows and 17 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') Empty PyRanges ('join', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain283-method_chain283] __________ [gw10] linux -- Python 3.12.6 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 880, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1722, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=('opposite', 'opposite'), | method_chain=('subtract', 'nearest'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=Empty PyRanges, | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:73 | (and 27 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2QAA0YGOEBiwtiMSGwAANEABw==') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 4384, in subtract | other_clusters = other.merge(strand=strand) | ^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 347, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=('opposite', 'opposite'), | method_chain=('subtract', 'nearest'), | gr=Empty PyRanges, | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=Empty PyRanges, # or any other generated value | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:143 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:30 | (and 19 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain270-method_chain270] __________ [gw3] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', 'opposite') method_chain = ('nearest', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('nearest', 'intersect'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:73 E (and 27 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2QAA0YGBGBEohgxZAEA3wAH') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 8 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain303-method_chain303] __________ [gw5] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = (False, None), method_chain = ('set_intersect', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('set_intersect', 'overlap'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 E (and 137 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BU0IuU8JcrYmBkwAIAKZIBoQ==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') __________ test_three_in_a_row[strandedness_chain316-method_chain316] __________ [gw1] linux -- Python 3.12.6 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 880, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1722, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 292, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=(False, None), | method_chain=('nearest', 'set_intersect'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 4 | 5 | a | 0 | - | | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=Empty PyRanges, | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:11 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:12 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:101 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 | (and 71 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY4zlfLadkYGRAQgYgQBMMzAwMzCB+QyMEDkwCWcguGAaAIc1AiE=') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3688, in set_intersect | other_clusters = other.merge(strand=strand) | ^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 381, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=(False, None), | method_chain=('nearest', 'set_intersect'), | gr=Empty PyRanges, | gr2=Empty PyRanges, # or any other generated value | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:38 | (and 163 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BAAEYUCgwAAD4AAw==') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty 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'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain227-method_chain227] __________ [gw4] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', 'same') method_chain = ('intersect', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('intersect', 'nearest'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:53 E (and 28 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2TAAIyMmGIMjJgcRgAA5QAH') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') __________ test_three_in_a_row[strandedness_chain237-method_chain237] __________ [gw7] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', 'same'), method_chain = ('subtract', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('subtract', 'join'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:30 E /usr/lib/python3/dist-packages/pandas/core/dtypes/missing.py:207 E (and 19 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAI4AxkAAABSAAM=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') __________ test_three_in_a_row[strandedness_chain306-method_chain306] __________ [gw6] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = (False, None), method_chain = ('set_intersect', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('set_intersect', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 E (and 178 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2Bk7H2Vm6nawMjAyIAJAEzpAvc=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') __________ test_three_in_a_row[strandedness_chain313-method_chain313] __________ [gw9] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = (False, None), method_chain = ('overlap', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('overlap', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:38 E (and 108 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BAAEYUCgwAAD4AAw==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') __________ test_three_in_a_row[strandedness_chain322-method_chain322] __________ [gw0] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = (False, None), method_chain = ('intersect', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('intersect', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:33 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E (and 218 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BAAEYUCgwAAD4AAw==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') __________ test_three_in_a_row[strandedness_chain284-method_chain284] __________ [gw10] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', 'opposite') method_chain = ('subtract', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('subtract', 'intersect'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:30 E /usr/lib/python3/dist-packages/pandas/core/dtypes/missing.py:207 E (and 18 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAI4AxkAAABSAAM=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') __________ test_three_in_a_row[strandedness_chain352-method_chain352] __________ [gw4] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', None), method_chain = ('set_intersect', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('set_intersect', 'overlap'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E /usr/lib/python3/dist-packages/natsort/utils.py:344 E (and 66 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2CAA0YGLAAAADUAAg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') __________ test_three_in_a_row[strandedness_chain327-method_chain327] __________ [gw3] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = (False, None), method_chain = ('intersect', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('intersect', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:38 E (and 109 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') __________ test_three_in_a_row[strandedness_chain307-method_chain307] __________ [gw6] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = (False, None), method_chain = ('set_intersect', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('set_intersect', 'join'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:38 E (and 137 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2CAA0YGLAAAADUAAg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') __________ test_three_in_a_row[strandedness_chain341-method_chain341] __________ [gw5] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = (False, None), method_chain = ('join', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('join', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:38 E (and 157 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') __________ test_three_in_a_row[strandedness_chain332-method_chain332] __________ [gw8] linux -- Python 3.12.6 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 880, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1722, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 292, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=(False, None), | method_chain=('subtract', 'nearest'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=Empty PyRanges, | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:53 | (and 29 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2TACxiRKCgbAACKAAU=') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 4384, in subtract | other_clusters = other.merge(strand=strand) | ^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 381, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=(False, None), | method_chain=('subtract', 'nearest'), | gr=Empty PyRanges, | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=Empty PyRanges, # or any other generated value | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:38 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 | (and 24 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 257 | 258 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain344-method_chain344] __________ [gw2] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', None) method_chain = ('set_union', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('set_union', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/init.py:174 E (and 189 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BU9Y6piRdwZ2BgZMAEADQqAgE=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') __________ test_three_in_a_row[strandedness_chain317-method_chain317] __________ [gw1] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = (False, None), method_chain = ('nearest', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:292: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('nearest', 'overlap'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:53 E (and 28 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2QAA0YGBGBEohgZ0OQBANYABw==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') __________ test_three_in_a_row[strandedness_chain336-method_chain336] __________ [gw7] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = (False, None), method_chain = ('join', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('join', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:33 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E (and 171 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') __________ test_three_in_a_row[strandedness_chain353-method_chain353] __________ [gw4] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', None), method_chain = ('set_intersect', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('set_intersect', 'nearest'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 E /usr/lib/python3/dist-packages/pandas/core/array_algos/take.py:574 E (and 61 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2DkDNX3L1X5wsjIgAUAADxtAm0=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') __________ test_three_in_a_row[strandedness_chain323-method_chain323] __________ [gw0] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = (False, None) method_chain = ('intersect', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('intersect', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:38 E (and 111 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') __________ test_three_in_a_row[strandedness_chain348-method_chain348] __________ [gw10] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', None), method_chain = ('set_union', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('set_union', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/init.py:174 E (and 187 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkiXX0U5WIY2BgZMAEACgHAY4=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') __________ test_three_in_a_row[strandedness_chain345-method_chain345] __________ [gw2] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', None), method_chain = ('set_union', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('set_union', 'overlap'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E (and 179 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2CAA0YGLAAAADUAAg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') __________ test_three_in_a_row[strandedness_chain308-method_chain308] __________ [gw6] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = (False, None), method_chain = ('overlap', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('overlap', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:33 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E (and 172 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') __________ test_three_in_a_row[strandedness_chain343-method_chain343] __________ [gw5] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', None), method_chain = ('set_union', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('set_union', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E (and 250 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2A0z65caST6lJGBkQETAABLsAL0') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') __________ test_three_in_a_row[strandedness_chain315-method_chain315] __________ [gw9] linux -- Python 3.12.6 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 880, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1722, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 292, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=(False, None), | method_chain=('nearest', 'set_union'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 65537 | 65538 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=Empty PyRanges, | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:11 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:12 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:101 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 | (and 64 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2SAAUZGOAuFQgcAAOgABg==') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3784, in set_union | gr = gr.merge(strand=strand) | ^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 360, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=(False, None), | method_chain=('nearest', 'set_union'), | gr=Empty PyRanges, | gr2=Empty PyRanges, # or any other generated value | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:33 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | (and 273 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BAAEYUCgwAAD4AAw==') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain333-method_chain333] __________ [gw8] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = (False, None), method_chain = ('subtract', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('subtract', 'intersect'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:38 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:369 E (and 23 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2 | 2503 | a | 0 | + | | chr1 | 2 | 2503 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') __________ test_three_in_a_row[strandedness_chain337-method_chain337] __________ [gw7] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = (False, None), method_chain = ('join', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('join', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:38 E (and 114 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') __________ test_three_in_a_row[strandedness_chain354-method_chain354] __________ [gw4] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', None) method_chain = ('set_intersect', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('set_intersect', 'intersect'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E (and 65 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2CAA0YGLAAAADUAAg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') __________ test_three_in_a_row[strandedness_chain318-method_chain318] __________ [gw1] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = (False, None), method_chain = ('nearest', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:63: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:292: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('nearest', 'nearest'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:53 E (and 30 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2TABIxIFCOqGAMDAACvAAY=') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') __________ test_three_in_a_row[strandedness_chain346-method_chain346] __________ [gw2] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', None), method_chain = ('set_union', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('set_union', 'nearest'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E (and 185 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2CAA0YGLAAAADUAAg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') __________ test_three_in_a_row[strandedness_chain329-method_chain329] __________ [gw3] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = (False, None), method_chain = ('subtract', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('subtract', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:38 E (and 207 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2CMjHq+J0dGlpGBkQETAABPkAL/') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') __________ test_three_in_a_row[strandedness_chain349-method_chain349] __________ [gw10] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', None), method_chain = ('set_union', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('set_union', 'join'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E (and 183 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2CAA0YGLAAAADUAAg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') __________ test_three_in_a_row[strandedness_chain334-method_chain334] __________ [gw8] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = (False, None), method_chain = ('subtract', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('subtract', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:38 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E (and 27 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAEECwEAAFEAAw==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') __________ test_three_in_a_row[strandedness_chain356-method_chain356] __________ [gw9] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', None), method_chain = ('set_intersect', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('set_intersect', 'join'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 E /usr/lib/python3/dist-packages/pandas/core/array_algos/take.py:574 E (and 61 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2CscJyW7ac4n4GRAQsAAEi1Ass=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') __________ test_three_in_a_row[strandedness_chain309-method_chain309] __________ [gw6] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = (False, None), method_chain = ('overlap', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('overlap', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:38 E (and 98 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') __________ test_three_in_a_row[strandedness_chain347-method_chain347] __________ [gw2] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', None), method_chain = ('set_union', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('set_union', 'intersect'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E (and 183 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2CAA0YGLAAAADUAAg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') __________ test_three_in_a_row[strandedness_chain325-method_chain325] __________ [gw0] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = (False, None), method_chain = ('intersect', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:292: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('intersect', 'nearest'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:73 E (and 27 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2TABIwoFIYQlA0AAN8ABw==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 65537 | 65559 | a | 0 | ... | | chr1 | 65537 | 65559 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 65537 | 65542 | a | 0 | ... | | chr1 | 65537 | 65541 | a | 0 | ... | | chr1 | 65537 | 65539 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 70 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 65537 | 65543 | a | 0 | ... | | chr1 | 65537 | 65541 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 65537 | 65541 | a | 0 | ... | | chr1 | 65537 | 65542 | a | 0 | ... | | chr1 | 65537 | 65542 | a | 0 | ... | | chr1 | 65537 | 65541 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 21 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 65538 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 65537 | 65538 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 14 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 10 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') __________ test_three_in_a_row[strandedness_chain355-method_chain355] __________ [gw4] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', None) method_chain = ('set_intersect', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('set_intersect', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:140 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E (and 107 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2CMtoq20VWYz8jAyIAJADZtAhw=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') __________ test_three_in_a_row[strandedness_chain350-method_chain350] __________ [gw10] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', None) method_chain = ('set_intersect', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('set_intersect', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:117 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E /usr/lib/python3/dist-packages/natsort/utils.py:344 E (and 128 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkDT4/n0v+NwMDIwMmAABKYALt') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') __________ test_three_in_a_row[strandedness_chain335-method_chain335] __________ [gw8] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = (False, None), method_chain = ('subtract', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('subtract', 'join'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:38 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E (and 24 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAI4AxkAAABSAAM=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +6 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 11 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 6 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') __________ test_three_in_a_row[strandedness_chain360-method_chain360] __________ [gw5] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', None), method_chain = ('overlap', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:292: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('overlap', 'nearest'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 258 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:73 E (and 27 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2QAAUYGKGCEsRhRhCEsJkaEGEKKgQEAAgUADQ==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 9757098 | 9757953 | a | 0 | ... | | chr1 | 9757098 | 9764756 | a | 0 | ... | | chr1 | 9757098 | 9763045 | a | 0 | ... | | chr1 | 8564321 | 8566161 | a | 0 | ... | | chr1 | 9757098 | 9758518 | a | 0 | ... | | chr1 | 9757098 | 9758472 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2036759 | 2038150 | a | 0 | ... | | chr1 | 4690863 | 4692391 | a | 0 | ... | | chr1 | 5941395 | 5949675 | a | 0 | ... | | chr1 | 4920148 | 4920626 | a | 0 | ... | | chr1 | 7923297 | 7928025 | a | 0 | ... | | chr1 | 275287 | 275435 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2036759 | 2038150 | a | 0 | ... | | chr1 | 4690863 | 4692391 | a | 0 | ... | | chr1 | 5941395 | 5949675 | a | 0 | ... | | chr1 | 4920148 | 4920626 | a | 0 | ... | | chr1 | 7923297 | 7928025 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 6214274 | 6216351 | a | 0 | ... | | chr1 | 7687991 | 7689359 | a | 0 | ... | | chr1 | 2357294 | 2359360 | a | 0 | ... | | chr1 | 1161824 | 1171338 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr8 | 3797839 | 3803022 | a | 0 | ... | | chr8 | 90177 | 93918 | a | 0 | ... | | chr10 | 6848303 | 6851003 | a | 0 | ... | | chr13 | 1626912 | 1628494 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 10 rows and 12 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 9 | 88 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 4 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 1529 | a | 0 | ... | | chr1 | 1 | 8281 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 1529 | a | 0 | ... | | chr1 | 1 | 8281 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 8281 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 8281 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 8281 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 8281 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 8281 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 7 | a | 0 | ... | | chr1 | 2 | 7 | a | 0 | ... | | chr1 | 2 | 7 | a | 0 | ... | | chr1 | 2 | 7 | a | 0 | ... | | chr1 | 2 | 7 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 7 | a | 0 | ... | | chr1 | 2 | 7 | a | 0 | ... | | chr1 | 2 | 7 | a | 0 | ... | | chr1 | 2 | 7 | a | 0 | ... | | chr1 | 2 | 7 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 7 | a | 0 | ... | | chr1 | 2 | 7 | a | 0 | ... | | chr1 | 2 | 7 | a | 0 | ... | | chr1 | 2 | 7 | a | 0 | ... | | chr1 | 2 | 7 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 7 | a | 0 | ... | | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 2 | 1530 | a | 0 | ... | | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 2 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 3 | a | 0 | ... | | chr1 | 1 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 3 | a | 0 | ... | | chr1 | 1 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain319-method_chain319] __________ [gw1] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = (False, None), method_chain = ('nearest', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:292: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('nearest', 'intersect'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:73 E (and 27 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2QAA0YGBGBEopDFIQAAANMABg==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain357-method_chain357] __________ [gw9] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', None), method_chain = ('overlap', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('overlap', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:33 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:41 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:17 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:21 E (and 142 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') __________ test_three_in_a_row[strandedness_chain330-method_chain330] __________ [gw3] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = (False, None), method_chain = ('subtract', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('subtract', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 E (and 189 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2DUZLjMV8FawcjAyIAJADOxAgM=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') __________ test_three_in_a_row[strandedness_chain339-method_chain339] __________ [gw7] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = (False, None), method_chain = ('join', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:68: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2, suffix="_c") pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:292: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('join', 'nearest'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:73 E (and 27 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2TABIy4xRiR2AAAwwAG') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 258 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') Empty PyRanges ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') __________ test_three_in_a_row[strandedness_chain376-method_chain376] __________ [gw2] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', None), method_chain = ('intersect', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('intersect', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:15 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:369 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:373 E (and 23 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BAAEYUCgwAAD4AAw==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 258 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | | chr1 | 6 | 258 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') __________ test_three_in_a_row[strandedness_chain364-method_chain364] __________ [gw6] linux -- Python 3.12.6 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 880, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1722, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', None), | method_chain=('nearest', 'set_union'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 65537 | 65541 | a | 0 | - | | | chr1 | 1 | 5 | a | 0 | - | | | chr1 | 1 | 5 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=Empty PyRanges, | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | (and 183 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY9Tq44lnlLFy2srIyAAEjECKkZEJxgRTIIKBGcSHCDAwwChGOI+BEQCrtwKO') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3784, in set_union | gr = gr.merge(strand=strand) | ^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 360, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', None), | method_chain=('nearest', 'set_union'), | gr=Empty PyRanges, | gr2=Empty PyRanges, # or any other generated value | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:33 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | (and 284 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain362-method_chain362] __________ [gw5] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', None), method_chain = ('overlap', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('overlap', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:38 E (and 106 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') __________ test_three_in_a_row[strandedness_chain351-method_chain351] __________ [gw10] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', None) method_chain = ('set_intersect', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('set_intersect', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:140 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E (and 107 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2CUd1xrpCbXzMjAyIAJADSkAgo=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') __________ test_three_in_a_row[strandedness_chain358-method_chain358] __________ [gw9] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', None), method_chain = ('overlap', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('overlap', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:38 E (and 109 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') __________ test_three_in_a_row[strandedness_chain366-method_chain366] __________ [gw0] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', None), method_chain = ('nearest', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('nearest', 'overlap'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:73 E (and 27 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2RAAowQkhGZB2XCOQAA6wAI') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 8 | 14 | a | 0 | ... | | chr2 | 1 | 4009 | a | 0 | ... | | chr2 | 1 | 9111 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') __________ test_three_in_a_row[strandedness_chain372-method_chain372] __________ [gw7] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', None) method_chain = ('intersect', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('intersect', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:15 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:145 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:369 E (and 23 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') __________ test_three_in_a_row[strandedness_chain369-method_chain369] __________ [gw4] linux -- Python 3.12.6 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 880, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1722, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', None), | method_chain=('nearest', 'subtract'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 258 | a | 0 | + | | | chr1 | 12 | 269 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=Empty PyRanges, | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:73 | (and 27 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY9Q1ONTCqD9ZdDMDIwMYMIJobkYQgAqBGCBREI8VRIHZUgxgJjOYYmAEAN7VA3M=') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 4384, in subtract | other_clusters = other.merge(strand=strand) | ^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 381, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', None), | method_chain=('nearest', 'subtract'), | gr=Empty PyRanges, | gr2=Empty PyRanges, # or any other generated value | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:15 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:369 | (and 24 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 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PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 258 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 258 | a | 0 | ... | | chr1 | 1 | 258 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 258 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain390-method_chain390] __________ [gw2] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', None), method_chain = ('join', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('join', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:15 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:369 E (and 24 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +6 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 11 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 6 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') __________ test_three_in_a_row[strandedness_chain378-method_chain378] __________ [gw3] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', None), method_chain = ('subtract', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('subtract', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:112 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:117 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 E (and 133 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2DMnBJQyMkSwMjAyIAJADjXAh8=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') __________ test_three_in_a_row[strandedness_chain381-method_chain381] __________ [gw8] linux -- Python 3.12.6 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 880, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1722, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 292, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', None), | method_chain=('subtract', 'nearest'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=Empty PyRanges, | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:53 | (and 29 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2RAAowM6IARUwIAAKgABQ==') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 4384, in subtract | other_clusters = other.merge(strand=strand) | ^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 347, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', None), | method_chain=('subtract', 'nearest'), | gr=Empty PyRanges, | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=Empty PyRanges, # or any other generated value | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:143 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:30 | (and 19 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 95 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 258 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 258 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain320-method_chain320] __________ [gw1] linux -- Python 3.12.6 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 880, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1722, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 292, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=(False, None), | method_chain=('nearest', 'subtract'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=Empty PyRanges, | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:53 | (and 30 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2QAA0YGBGCEkowoMnAVAAD4AAg=') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 4384, in subtract | other_clusters = other.merge(strand=strand) | ^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 381, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=(False, None), | method_chain=('nearest', 'subtract'), | gr=Empty PyRanges, | gr2=Empty PyRanges, # or any other generated value | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:38 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 | (and 24 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 258 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain383-method_chain383] __________ [gw10] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', None), method_chain = ('subtract', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('subtract', 'subtract'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:30 E (and 19 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 65537 | 65538 | a | 0 | + | | chr1 | 65537 | 65538 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') __________ test_three_in_a_row[strandedness_chain388-method_chain388] __________ [gw5] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', None), method_chain = ('join', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:68: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2, suffix="_c") pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:292: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('join', 'nearest'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:53 E (and 29 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2TABIy4xRiR2AAAwwAG') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr19 | 7150710 | 7150967 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 65538 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4198112 | 4198369 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') __________ test_three_in_a_row[strandedness_chain397-method_chain397] __________ [gw9] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', None) method_chain = ('set_union', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('set_union', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/init.py:174 E (and 201 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2AMjYjcHaIQzsDAyIAJAEL4Ao8=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') __________ test_three_in_a_row[strandedness_chain382-method_chain382] __________ [gw8] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', None), method_chain = ('subtract', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('subtract', 'intersect'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:30 E /usr/lib/python3/dist-packages/pandas/core/dtypes/missing.py:207 E (and 18 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') __________ test_three_in_a_row[strandedness_chain365-method_chain365] __________ [gw6] linux -- Python 3.12.6 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 880, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1722, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', None), | method_chain=('nearest', 'set_intersect'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | | chr1 | 3 | 4 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=Empty PyRanges, | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | (and 185 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2QAAkZGBgZxIAWEQCAIFpHXZX7MmKkz3woqzMgoApLUZmBgAmuBqIVIAREAgbEDGw==') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3688, in set_intersect | other_clusters = other.merge(strand=strand) | ^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 381, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', None), | method_chain=('nearest', 'set_intersect'), | gr=Empty PyRanges, | gr2=Empty PyRanges, # or any other generated value | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:38 | (and 167 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain385-method_chain385] __________ [gw1] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', None), method_chain = ('join', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('join', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:33 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:41 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:17 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:21 E (and 96 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') __________ test_three_in_a_row[strandedness_chain370-method_chain370] __________ [gw4] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', None), method_chain = ('nearest', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:63: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('nearest', 'join'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:73 E (and 27 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2QAA0YGOGBkRBJihDIZFQQ++/jwLGEAAAw5AnQ=') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') __________ test_three_in_a_row[strandedness_chain392-method_chain392] __________ [gw2] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', None) method_chain = ('set_union', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('set_union', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E (and 263 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2D0VDFWLpWfwcjAyIAJADGIAfM=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') __________ test_three_in_a_row[strandedness_chain367-method_chain367] __________ [gw0] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', None), method_chain = ('nearest', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:63: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('nearest', 'nearest'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:53 E (and 29 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2RAAozYKHQAAAC+AAU=') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain379-method_chain379] __________ [gw3] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', None) method_chain = ('subtract', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('subtract', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:112 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:117 E (and 120 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkTDffmiTBxsDAyIAJADA9Adc=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') __________ test_three_in_a_row[strandedness_chain374-method_chain374] __________ [gw7] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', None), method_chain = ('intersect', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:292: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('intersect', 'nearest'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 3 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | - | E | chr1 | 2 | 3 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:73 E (and 27 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2QAA0YGBhiDkREmwIjCQyMZ0TQCAQADCAAR') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 182273 | 184842 | a | 0 | ... | | chr1 | 7538090 | 7538228 | a | 0 | ... | | chr1 | 9041528 | 9042602 | a | 0 | ... | | chr1 | 1562543 | 1570082 | a | 0 | ... | | chr14 | 5425539 | 5427152 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 182273 | 184842 | a | 0 | ... | | chr1 | 7538090 | 7538228 | a | 0 | ... | | chr1 | 9041528 | 9042602 | a | 0 | ... | | chr1 | 1562543 | 1570082 | a | 0 | ... | | chr14 | 5425539 | 5427152 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1784832 | 1791357 | a | 0 | ... | | chr1 | 1238402 | 1238659 | a | 0 | ... | | chr1 | 6000472 | 6000729 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 5 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 5 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 5 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 5 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 5 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 6 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 6 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 4 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 4 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 4 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 4 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr2 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr2 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 3 | a | 0 | ... | | chr1 | 1 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 3 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain384-method_chain384] __________ [gw10] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', None), method_chain = ('subtract', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('subtract', 'join'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:30 E (and 19 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2CAA0YUCgIAAEAAAw==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +6 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 258 | a | 0 | ... | | chr1 | 1 | 258 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 11 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 6 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') __________ test_three_in_a_row[strandedness_chain402-method_chain402] __________ [gw8] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', None) method_chain = ('set_intersect', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('set_intersect', 'nearest'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 E /usr/lib/python3/dist-packages/pandas/core/array_algos/take.py:574 E (and 61 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2CAA0YGLAAAADUAAg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') __________ test_three_in_a_row[strandedness_chain398-method_chain398] __________ [gw9] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', None), method_chain = ('set_union', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('set_union', 'join'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E (and 197 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2CsYmBgyJBsZGBkwAIAJjsBfw==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') __________ test_three_in_a_row[strandedness_chain395-method_chain395] __________ [gw5] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', None), method_chain = ('set_union', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('set_union', 'nearest'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E (and 198 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2DkyjaJspdZxMjIgAUAADMzAgQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') __________ test_three_in_a_row[strandedness_chain401-method_chain401] __________ [gw2] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', None) method_chain = ('set_intersect', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('set_intersect', 'overlap'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E /usr/lib/python3/dist-packages/natsort/utils.py:344 E (and 66 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2DMn6orFCr5jZGRAQsAAESZAqs=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') __________ test_three_in_a_row[strandedness_chain403-method_chain403] __________ [gw10] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', None) method_chain = ('set_intersect', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('set_intersect', 'intersect'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E (and 65 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2CAA0YGLAAAADUAAg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') __________ test_three_in_a_row[strandedness_chain386-method_chain386] __________ [gw1] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', None), method_chain = ('join', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('join', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:38 E (and 160 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') __________ test_three_in_a_row[strandedness_chain393-method_chain393] __________ [gw6] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', None) method_chain = ('set_union', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('set_union', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/init.py:174 E (and 205 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2Bk8FHvz+C9zMDAyIAJADmZAk0=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') __________ test_three_in_a_row[strandedness_chain371-method_chain371] __________ [gw4] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', None), method_chain = ('intersect', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('intersect', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:33 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:41 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:17 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:21 E (and 143 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') __________ test_three_in_a_row[strandedness_chain405-method_chain405] __________ [gw8] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', None) method_chain = ('set_intersect', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('set_intersect', 'join'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 E /usr/lib/python3/dist-packages/pandas/core/array_algos/take.py:574 E /usr/lib/python3/dist-packages/pandas/core/common.py:143 E (and 62 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2AM1AvxrOS3Z2RkwAIAMcUB5w==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') __________ test_three_in_a_row[strandedness_chain380-method_chain380] __________ [gw3] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', None), method_chain = ('subtract', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('subtract', 'overlap'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:30 E /usr/lib/python3/dist-packages/pandas/core/dtypes/missing.py:207 E (and 18 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAI4AxkAAABSAAM=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') __________ test_three_in_a_row[strandedness_chain396-method_chain396] __________ [gw5] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', None) method_chain = ('set_union', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('set_union', 'intersect'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E (and 196 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2Bkm/Y/2JU5k4GRAQsAAEUvAqI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') __________ test_three_in_a_row[strandedness_chain399-method_chain399] __________ [gw7] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', None) method_chain = ('set_intersect', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('set_intersect', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:117 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E /usr/lib/python3/dist-packages/natsort/utils.py:344 E (and 126 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2AMio+bVKvOz8DAyIAJAD3zAlc=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') __________ test_three_in_a_row[strandedness_chain368-method_chain368] __________ [gw0] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('same', None), method_chain = ('nearest', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('nearest', 'intersect'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:53 E (and 30 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2TABIzYOIziigkJ8TwZjAAIzAHR') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') __________ test_three_in_a_row[strandedness_chain404-method_chain404] __________ [gw9] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', None) method_chain = ('set_intersect', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('set_intersect', 'subtract'), E gr=Empty PyRanges, # or any other generated value E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:140 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E (and 109 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BAAEYGTAAAADQAAg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') __________ test_three_in_a_row[strandedness_chain411-method_chain411] __________ [gw10] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', None), method_chain = ('overlap', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('overlap', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:38 E (and 105 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') __________ test_three_in_a_row[strandedness_chain394-method_chain394] __________ [gw6] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', None), method_chain = ('set_union', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('set_union', 'overlap'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E (and 195 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2CAA0YGLAAAADUAAg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') __________ test_three_in_a_row[strandedness_chain407-method_chain407] __________ [gw4] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', None) method_chain = ('overlap', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('overlap', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:38 E (and 106 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') __________ test_three_in_a_row[strandedness_chain406-method_chain406] __________ [gw1] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', None), method_chain = ('overlap', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('overlap', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:33 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E (and 220 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') __________ test_three_in_a_row[strandedness_chain421-method_chain421] __________ [gw8] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', None) method_chain = ('intersect', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('intersect', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:15 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:145 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:369 E (and 23 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') __________ test_three_in_a_row[strandedness_chain400-method_chain400] __________ [gw7] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', None) method_chain = ('set_intersect', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('set_intersect', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:140 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E (and 106 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2DULMvO8eW8xMjAyIAJAENwAqI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') __________ test_three_in_a_row[strandedness_chain415-method_chain415] __________ [gw2] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', None), method_chain = ('nearest', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('nearest', 'overlap'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:73 E (and 27 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2QAA0YGBGCEkoyoPC4DqwRf9peMAAj7Ahs=') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 74563 | a | 0 | ... | | chr1 | 65537 | 74563 | a | 0 | ... | | chr1 | 65537 | 74563 | a | 0 | ... | | chr1 | 65537 | 74563 | a | 0 | ... | | chr1 | 65537 | 74563 | a | 0 | ... | | chr1 | 65537 | 74563 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty 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('nearest', 'overlap') ('nearest', 'overlap') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain414-method_chain414] __________ [gw5] linux -- Python 3.12.6 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 880, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1722, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=('opposite', None), | method_chain=('nearest', 'set_intersect'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=Empty PyRanges, | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | (and 173 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2QAAUYgRABGRhRBmBSjqOLr16pqwQwADp8CtA==') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3688, in set_intersect | other_clusters = other.merge(strand=strand) | ^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 381, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=('opposite', None), | method_chain=('nearest', 'set_intersect'), | gr=Empty PyRanges, | gr2=Empty PyRanges, | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:38 | (and 159 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BAAEYUCgwAAD4AAw==') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges 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'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges 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('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges 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('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain428-method_chain428] __________ [gw3] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', None) method_chain = ('subtract', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('subtract', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:112 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:117 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:140 E (and 120 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2DktpnDo87Fz8jAyIAJAB/6ATM=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') 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('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') _____________________________ test_introns_single ______________________________ [gw5] linux -- Python 3.12.6 /usr/bin/python3.12 def test_introns_single(): "Assert that our fast method of computing introns is the same as the slow, correct one in compute_introns_single" gr = pr.data.gencode_gtf()[["gene_id", "Feature"]] exons = gr[gr.Feature == "exon"].merge(by="gene_id") exons.Feature = "exon" exons = exons.df df = pd.concat([gr[gr.Feature == "gene"].df, exons], sort=False) print(df) for gid, gdf in df.groupby("gene_id"): print("-------" * 20) print(gid) print(gdf) print("gdf", len(gdf)) expected = compute_introns_single(gdf, by="gene") print("expected", len(expected)) > actual = pr.PyRanges(gdf).features.introns().df tests/test_genomicfeatures.py:174: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ pyranges/genomicfeatures.py:254: in introns result = pyrange_apply(_introns2, by_gr, exons, **kwargs) pyranges/multithreaded.py:292: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/genomicfeatures.py:567: in _introns2 starts, ends, ids = find_introns(genes.Start.values, genes.End.values, _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' sorted_nearest/src/introns.pyx:12: ValueError ----------------------------- Captured stdout call ----------------------------- Chromosome gene_id Start End Strand Feature 0 chr1 ENSG00000223972.5 11868 14409 + gene 1 chr1 ENSG00000243485.5 29553 31109 + gene 2 chr1 ENSG00000284332.1 30365 30503 + gene 3 chr1 ENSG00000268020.3 52472 53312 + gene 4 chr1 ENSG00000240361.2 57597 64116 + gene .. ... ... ... ... ... ... 587 chr1 ENSG00000283040.1 876754 877234 - exon 588 chr1 ENSG00000283712.1 1312501 1312566 - exon 589 chr1 ENSG00000284372.1 1339649 1339708 - exon 590 chr1 ENSG00000284662.1 685678 686673 - exon 591 chr1 ENSG00000284733.1 450702 451697 - exon [711 rows x 6 columns] -------------------------------------------------------------------------------------------------------------------------------------------- ENSG00000078808.16 Chromosome gene_id Start End Strand Feature 101 chr1 ENSG00000078808.16 1216907 1232031 - gene 284 chr1 ENSG00000078808.16 1216907 1217804 - exon 285 chr1 ENSG00000078808.16 1218457 1221351 - exon 286 chr1 ENSG00000078808.16 1223243 1223357 - exon 287 chr1 ENSG00000078808.16 1223831 1223968 - exon 288 chr1 ENSG00000078808.16 1227271 1227319 - exon 289 chr1 ENSG00000078808.16 1228467 1228946 - exon 290 chr1 ENSG00000078808.16 1231891 1232031 - exon gdf 8 g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g Chromosome gene_id Start End Strand Feature 101 chr1 ENSG00000078808.16 1216907 1232031 - gene x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x Chromosome Start End gene_id Strand 0 chr1 1216907 1217804 ENSG00000078808.16 - 1 chr1 1218457 1221351 ENSG00000078808.16 - 2 chr1 1223243 1223357 ENSG00000078808.16 - 3 chr1 1223831 1223968 ENSG00000078808.16 - 4 chr1 1227271 1227319 ENSG00000078808.16 - 5 chr1 1228467 1228946 ENSG00000078808.16 - 6 chr1 1231891 1232031 ENSG00000078808.16 - expected 6 __________ test_three_in_a_row[strandedness_chain427-method_chain427] __________ [gw0] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', None) method_chain = ('subtract', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('subtract', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:112 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:117 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:342 E (and 134 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BMM5NJDZQqYGRgZMAEADN8Afw=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain413-method_chain413] __________ [gw9] linux -- Python 3.12.6 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 880, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1722, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=('opposite', None), | method_chain=('nearest', 'set_union'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2512 | 2513 | a | 0 | + | | | chr1 | 2512 | 2513 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=Empty PyRanges, | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:39 | (and 170 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2QAAkYG1/ttQBIE9Rg4z0PEGEEEA4SNFQAAgX8Cug==') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3784, in set_union | gr = gr.merge(strand=strand) | ^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 360, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=('opposite', None), | method_chain=('nearest', 'set_union'), | gr=Empty PyRanges, | gr2=Empty PyRanges, # or any other generated value | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:33 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 | (and 274 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BAAEYUCgwAAD4AAw==') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain425-method_chain425] __________ [gw8] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', None) method_chain = ('intersect', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('intersect', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:15 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:145 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:369 E (and 23 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') __________ test_three_in_a_row[strandedness_chain420-method_chain420] __________ [gw4] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', None) method_chain = ('intersect', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('intersect', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:33 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:41 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:13 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:17 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:21 E (and 144 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') _______________________________ test_merge[True] _______________________________ [gw5] linux -- Python 3.12.6 /usr/bin/python3.12 strand = True @pytest.mark.bedtools > @pytest.mark.parametrize("strand", [True, False]) tests/test_unary.py:31: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_unary.py:75: in test_merge result = gr.merge(strand=strand, count=True) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_merge( E strand=True, E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., # or any other generated value E ) sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpavgbnt_k/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1 2 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1888652 | 1896208 | a | 0 | + | | chr1 | 4036435 | 4043057 | a | 0 | + | | chr1 | 3494892 | 3499585 | a | 0 | - | | chr1 | 6788882 | 6795601 | a | 0 | - | | chr1 | 9949892 | 9954396 | a | 0 | - | | chr15 | 4643057 | 4645647 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmptc42f3jm/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1888652 1896208 + 1 chr1 3494892 3499585 - 1 chr1 4036435 4043057 + 1 chr1 6788882 6795601 - 1 chr1 9949892 9954396 - 1 chr15 4643057 4645647 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1888652 1896208 + 1 1 chr1 3494892 3499585 - 1 2 chr1 4036435 4043057 + 1 3 chr1 6788882 6795601 - 1 4 chr1 9949892 9954396 - 1 5 chr15 4643057 4645647 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1888652 | 1896208 | a | 0 | + | | chr1 | 4036435 | 4043057 | a | 0 | + | | chr1 | 3494892 | 3499585 | a | 0 | - | | chr1 | 6788882 | 6795601 | a | 0 | - | | chr1 | 9949892 | 9954396 | a | 0 | - | | chr15 | 4643057 | 4645647 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpf84w21zs/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1888652 1896208 + 1 chr1 3494892 3499585 - 1 chr1 4036435 4043057 + 1 chr1 6788882 6795601 - 1 chr1 9949892 9954396 - 1 chr15 4643057 4645647 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1888652 1896208 + 1 1 chr1 3494892 3499585 - 1 2 chr1 4036435 4043057 + 1 3 chr1 6788882 6795601 - 1 4 chr1 9949892 9954396 - 1 5 chr15 4643057 4645647 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7556 | 15112 | a | 0 | + | | chr1 | 6622 | 13244 | a | 0 | + | | chr1 | 4693 | 9386 | a | 0 | - | | chr1 | 6719 | 13438 | a | 0 | - | | chr1 | 4504 | 9008 | a | 0 | - | | chr15 | 2590 | 5180 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp7h9kvr5o/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 4504 13438 - 3 chr1 6622 15112 + 2 chr15 2590 5180 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 4504 13438 - 3 1 chr1 6622 15112 + 2 2 chr15 2590 5180 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4693 | 9386 | a | 0 | - | | chr1 | 7556 | 15112 | a | 0 | - | | chr1 | 6719 | 13438 | a | 0 | - | | chr1 | 6622 | 13244 | a | 0 | - | | chr1 | 4504 | 9008 | a | 0 | - | | chr15 | 2590 | 5180 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpmbsn28nl/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 4504 15112 - 5 chr15 2590 5180 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 4504 15112 - 5 1 chr15 2590 5180 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4693 | 9197 | a | 0 | + | | chr1 | 4693 | 4694 | a | 0 | - | | chr1 | 4693 | 11412 | a | 0 | - | | chr1 | 4693 | 11315 | a | 0 | - | | chr15 | 4693 | 7283 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpq6fheks9/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 4693 11412 - 3 chr1 4693 9197 + 1 chr15 4693 7283 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 4693 11412 - 3 1 chr1 4693 9197 + 1 2 chr15 4693 7283 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4693 | 9197 | a | 0 | + | | chr1 | 4693 | 4694 | a | 0 | + | | chr1 | 4693 | 11412 | a | 0 | + | | chr15 | 4693 | 7283 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp8tpmards/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 4693 11412 + 3 chr15 4693 7283 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 4693 11412 + 3 1 chr15 4693 7283 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3303416 | 3308967 | a | 0 | + | | chr1 | 6143439 | 6146627 | a | 0 | - | | chr3 | 2873765 | 2880910 | a | 0 | + | | chr3 | 3303416 | 3306575 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr6 | 5935913 | 5943058 | a | 0 | + | | chr6 | 3303416 | 3310561 | a | 0 | + | | chr7 | 3304853 | 3311998 | a | 0 | + | | chr14 | 2611985 | 2614440 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 10 rows and 6 columns from 7 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpdoig8s4y/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 3303416 3308967 + 1 chr1 6143439 6146627 - 1 chr14 2611985 2614440 + 1 chr22 5394305 5401450 - 1 chr3 2873765 2880910 + 1 chr3 3303416 3306575 + 1 chr4 3303416 3305711 - 1 chr6 3303416 3310561 + 1 chr6 5935913 5943058 + 1 chr7 3304853 3311998 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 3303416 3308967 + 1 1 chr1 6143439 6146627 - 1 2 chr14 2611985 2614440 + 1 3 chr22 5394305 5401450 - 1 4 chr3 2873765 2880910 + 1 5 chr3 3303416 3306575 + 1 6 chr4 3303416 3305711 - 1 7 chr6 3303416 3310561 + 1 8 chr6 5935913 5943058 + 1 9 chr7 3304853 3311998 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3303416 | 3308967 | a | 0 | + | | chr1 | 6143439 | 6146627 | a | 0 | - | | chr3 | 2873765 | 2880910 | a | 0 | + | | chr3 | 3303416 | 3306575 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr6 | 5935913 | 5943058 | a | 0 | + | | chr6 | 3303416 | 3310561 | a | 0 | + | | chr7 | 3304853 | 3311998 | a | 0 | + | | chr14 | 2611985 | 2614440 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 10 rows and 6 columns from 7 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpo4j_7s9l/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 3303416 3308967 + 1 chr1 6143439 6146627 - 1 chr14 2611985 2614440 + 1 chr22 5394305 5401450 - 1 chr3 2873765 2880910 + 1 chr3 3303416 3306575 + 1 chr4 3303416 3305711 - 1 chr6 3303416 3310561 + 1 chr6 5935913 5943058 + 1 chr7 3304853 3311998 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 3303416 3308967 + 1 1 chr1 6143439 6146627 - 1 2 chr14 2611985 2614440 + 1 3 chr22 5394305 5401450 - 1 4 chr3 2873765 2880910 + 1 5 chr3 3303416 3306575 + 1 6 chr4 3303416 3305711 - 1 7 chr6 3303416 3310561 + 1 8 chr6 5935913 5943058 + 1 9 chr7 3304853 3311998 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpkr3_eans/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1 2 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp8jqz3ogm/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1 2 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpf4_6de2h/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1 2 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpz6so8l1j/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1 2 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpxvz7g1p6/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1 2 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2843794 | 2847992 | a | 0 | + | | chr1 | 2274796 | 2282161 | a | 0 | + | | chr1 | 6527854 | 6527855 | a | 0 | - | | chr1 | 6401803 | 6411272 | a | 0 | - | | chr5 | 8321641 | 8322222 | a | 0 | + | | chr7 | 584103 | 587229 | a | 0 | + | | chr7 | 7402166 | 7403846 | a | 0 | - | | chr11 | 8590403 | 8593731 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 8 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp6wim4j5z/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2274796 2282161 + 1 chr1 2843794 2847992 + 1 chr1 6401803 6411272 - 1 chr1 6527854 6527855 - 1 chr11 8590403 8593731 - 1 chr5 8321641 8322222 + 1 chr7 584103 587229 + 1 chr7 7402166 7403846 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 2274796 2282161 + 1 1 chr1 2843794 2847992 + 1 2 chr1 6401803 6411272 - 1 3 chr1 6527854 6527855 - 1 4 chr11 8590403 8593731 - 1 5 chr5 8321641 8322222 + 1 6 chr7 584103 587229 + 1 7 chr7 7402166 7403846 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr9 | 7004247 | 7006398 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpqeouu1ut/f1.bed) resultresultresultresultresultresultresultresultresultresult chr9 7004247 7006398 + 1 bedtools_df Chromosome Start End Strand Count 0 chr9 7004247 7006398 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7534902 | 7536005 | a | 0 | + | | chr8 | 4259666 | 4261630 | a | 0 | + | | chr15 | 9200576 | 9203508 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpy1otwdbi/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 7534902 7536005 + 1 chr15 9200576 9203508 - 1 chr8 4259666 4261630 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 7534902 7536005 + 1 1 chr15 9200576 9203508 - 1 2 chr8 4259666 4261630 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5329266 | 5339266 | a | 0 | + | | chr1 | 5145760 | 5147469 | a | 0 | + | | chr5 | 1689994 | 1698370 | a | 0 | + | | chr5 | 5145760 | 5147684 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr11 | 7930749 | 7934553 | a | 0 | + | | chr12 | 7043071 | 7049120 | a | 0 | - | | chr12 | 3750500 | 3752424 | a | 0 | - | | chr19 | 6187247 | 6187543 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 9 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp25adn_3e/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 5145760 5147469 + 1 chr1 5329266 5339266 + 1 chr11 7930749 7934553 + 1 chr12 3750500 3752424 - 1 chr12 7043071 7049120 - 1 chr19 6187247 6187543 - 1 chr5 1689994 1698370 + 1 chr5 5145760 5147684 + 1 chr7 7862353 7864277 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 5145760 5147469 + 1 1 chr1 5329266 5339266 + 1 2 chr11 7930749 7934553 + 1 3 chr12 3750500 3752424 - 1 4 chr12 7043071 7049120 - 1 5 chr19 6187247 6187543 - 1 6 chr5 1689994 1698370 + 1 7 chr5 5145760 5147684 + 1 8 chr7 7862353 7864277 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9118319 | 9118744 | a | 0 | + | | chr1 | 3300895 | 3307296 | a | 0 | + | | chr1 | 6376024 | 6381485 | a | 0 | + | | chr1 | 8209437 | 8215838 | a | 0 | - | | chr1 | 10000000 | 10008083 | a | 0 | - | | chr6 | 8604746 | 8611147 | a | 0 | + | | chr6 | 8822808 | 8828020 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 7 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpnst3zfn8/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 3300895 3307296 + 1 chr1 6376024 6381485 + 1 chr1 8209437 8215838 - 1 chr1 9118319 9118744 + 1 chr1 10000000 10008083 - 1 chr6 8604746 8611147 + 1 chr6 8822808 8828020 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 3300895 3307296 + 1 1 chr1 6376024 6381485 + 1 2 chr1 8209437 8215838 - 1 3 chr1 9118319 9118744 + 1 4 chr1 10000000 10008083 - 1 5 chr6 8604746 8611147 + 1 6 chr6 8822808 8828020 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 223093 | 229013 | a | 0 | - | | chr21 | 9600917 | 9608414 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpm42z9q0b/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 223093 229013 - 1 chr21 9600917 9608414 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 223093 229013 - 1 1 chr21 9600917 9608414 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3123804 | 3130727 | a | 0 | + | | chr1 | 4700672 | 4700985 | a | 0 | + | | chr1 | 10000000 | 10008631 | a | 0 | - | | chr1 | 1524405 | 1530657 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr1 | 1524405 | 1530657 | a | 0 | - | | chr1 | 2064227 | 2067176 | a | 0 | - | | chr1 | 9096045 | 9099269 | a | 0 | - | | chr1 | 8717145 | 8718442 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 10 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpuz6bodz8/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1524405 1530657 - 1 chr1 2064227 2067176 - 1 chr1 3123804 3130727 + 1 chr1 4700672 4700985 + 1 chr1 8717145 8718442 - 1 chr1 9096045 9099269 - 1 chr1 10000000 10008631 - 1 chr14 7061032 7062700 + 1 chr15 3111135 3117187 + 1 chr20 2879197 2879212 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1524405 1530657 - 1 1 chr1 2064227 2067176 - 1 2 chr1 3123804 3130727 + 1 3 chr1 4700672 4700985 + 1 4 chr1 8717145 8718442 - 1 5 chr1 9096045 9099269 - 1 6 chr1 10000000 10008631 - 1 7 chr14 7061032 7062700 + 1 8 chr15 3111135 3117187 + 1 9 chr20 2879197 2879212 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7426474 | 7427163 | a | 0 | + | | chr1 | 6338415 | 6341600 | a | 0 | + | | chr1 | 4981432 | 4981780 | a | 0 | + | | chr1 | 4532309 | 4536706 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr1 | 4532309 | 4536706 | a | 0 | + | | chr1 | 9175110 | 9175333 | a | 0 | - | | chr1 | 4385918 | 4388070 | a | 0 | - | | chr1 | 9535856 | 9535858 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 9 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpws9s22jf/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 4385918 4388070 - 1 chr1 4532309 4536706 + 1 chr1 4981432 4981780 + 1 chr1 6338415 6341600 + 1 chr1 7426474 7427163 + 1 chr1 9175110 9175333 - 1 chr1 9535856 9535858 - 1 chr20 2678772 2683702 - 1 chr4 4385918 4390848 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 4385918 4388070 - 1 1 chr1 4532309 4536706 + 1 2 chr1 4981432 4981780 + 1 3 chr1 6338415 6341600 + 1 4 chr1 7426474 7427163 + 1 5 chr1 9175110 9175333 - 1 6 chr1 9535856 9535858 - 1 7 chr20 2678772 2683702 - 1 8 chr4 4385918 4390848 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1725991 | 1727536 | a | 0 | - | | chr7 | 2399966 | 2408755 | a | 0 | - | | chr17 | 8967887 | 8977006 | a | 0 | - | | chrY | 4424813 | 4427169 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpgkluh_8a/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1725991 1727536 - 1 chr17 8967887 8977006 - 1 chr7 2399966 2408755 - 1 chrY 4424813 4427169 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1725991 1727536 - 1 1 chr17 8967887 8977006 - 1 2 chr7 2399966 2408755 - 1 3 chrY 4424813 4427169 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8465891 | 8475558 | a | 0 | + | | chr1 | 9647537 | 9654755 | a | 0 | + | | chr1 | 8184373 | 8190139 | a | 0 | + | | chr1 | 6811902 | 6812082 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr4 | 8219868 | 8225306 | a | 0 | + | | chr4 | 2658811 | 2664246 | a | 0 | + | | chr9 | 5024556 | 5025357 | a | 0 | + | | chr9 | 2502681 | 2510462 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpxbeuw402/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 6206549 6210867 + 1 chr1 6811902 6812082 + 1 chr1 7788601 7791786 - 1 chr1 8184373 8190139 + 1 chr1 8465891 8475558 + 1 chr1 9647537 9654755 + 1 chr17 8951068 8953043 + 1 chr4 2658811 2664246 + 1 chr4 8219868 8225306 + 1 chr9 2502681 2510462 - 1 chr9 5024556 5025357 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 6206549 6210867 + 1 1 chr1 6811902 6812082 + 1 2 chr1 7788601 7791786 - 1 3 chr1 8184373 8190139 + 1 4 chr1 8465891 8475558 + 1 5 chr1 9647537 9654755 + 1 6 chr17 8951068 8953043 + 1 7 chr4 2658811 2664246 + 1 8 chr4 8219868 8225306 + 1 9 chr9 2502681 2510462 - 1 10 chr9 5024556 5025357 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3917934 | 3919716 | a | 0 | + | | chr1 | 176192 | 180281 | a | 0 | + | | chr1 | 5618800 | 5621603 | a | 0 | + | | chr1 | 176192 | 183594 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr15 | 176192 | 185522 | a | 0 | + | | chr17 | 176192 | 178132 | a | 0 | + | | chr18 | 8776346 | 8783390 | a | 0 | + | | chrX | 176192 | 178007 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpuh8opz8x/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 176192 183594 + 2 chr1 176192 184628 - 1 chr1 1504714 1512261 - 1 chr1 3917934 3919716 + 1 chr1 5618800 5621603 + 1 chr15 176192 185522 + 1 chr17 176192 178132 + 1 chr18 8776346 8783390 + 1 chr6 176192 184669 + 1 chrX 176192 178007 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 176192 183594 + 2 1 chr1 176192 184628 - 1 2 chr1 1504714 1512261 - 1 3 chr1 3917934 3919716 + 1 4 chr1 5618800 5621603 + 1 5 chr15 176192 185522 + 1 6 chr17 176192 178132 + 1 7 chr18 8776346 8783390 + 1 8 chr6 176192 184669 + 1 9 chrX 176192 178007 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7517869 | 7523921 | a | 0 | + | | chr1 | 6325275 | 6328199 | a | 0 | + | | chr9 | 3301739 | 3307783 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp3mwkkn1i/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 6325275 6328199 + 1 chr1 7517869 7523921 + 1 chr9 3301739 3307783 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 6325275 6328199 + 1 1 chr1 7517869 7523921 + 1 2 chr9 3301739 3307783 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1729422 | 1729897 | a | 0 | + | | chr1 | 327950 | 328425 | a | 0 | + | | chr1 | 4276144 | 4276619 | a | 0 | + | | chr1 | 407288 | 407763 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr11 | 1729422 | 1729897 | a | 0 | + | | chr14 | 1729422 | 1729897 | a | 0 | - | | chr20 | 2447447 | 2454435 | a | 0 | + | | chrY | 10000000 | 10000475 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 8 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmplrrih1ow/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 327950 328425 + 1 chr1 407288 407763 - 1 chr1 1729422 1729897 + 1 chr1 4276144 4276619 + 1 chr10 6267184 6267659 + 1 chr11 1729422 1729897 + 1 chr14 1729422 1729897 - 1 chr20 2447447 2454435 + 1 chr4 9142370 9142845 + 1 chr9 116705 117180 - 1 chrY 10000000 10000475 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 327950 328425 + 1 1 chr1 407288 407763 - 1 2 chr1 1729422 1729897 + 1 3 chr1 4276144 4276619 + 1 4 chr10 6267184 6267659 + 1 5 chr11 1729422 1729897 + 1 6 chr14 1729422 1729897 - 1 7 chr20 2447447 2454435 + 1 8 chr4 9142370 9142845 + 1 9 chr9 116705 117180 - 1 10 chrY 10000000 10000475 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4458131 | 4464169 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpoz97x4kr/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 4458131 4464169 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 4458131 4464169 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6135143 | 6140628 | a | 0 | + | | chr1 | 5603219 | 5608729 | a | 0 | + | | chr1 | 4331507 | 4340876 | a | 0 | + | | chr1 | 6543646 | 6548158 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr16 | 5859083 | 5868714 | a | 0 | - | | chr17 | 5859083 | 5867387 | a | 0 | - | | chr18 | 5859083 | 5866832 | a | 0 | + | | chr20 | 1213189 | 1221186 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 10 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpc_iq3pyd/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2060828 2061071 - 1 chr1 4331507 4340876 + 1 chr1 5603219 5608729 + 1 chr1 6135143 6140628 + 1 chr1 6543646 6548158 - 1 chr1 9736907 9745461 - 1 chr16 5859083 5868714 - 1 chr17 5859083 5867387 - 1 chr18 5859083 5866832 + 1 chr20 1213189 1221186 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 2060828 2061071 - 1 1 chr1 4331507 4340876 + 1 2 chr1 5603219 5608729 + 1 3 chr1 6135143 6140628 + 1 4 chr1 6543646 6548158 - 1 5 chr1 9736907 9745461 - 1 6 chr16 5859083 5868714 - 1 7 chr17 5859083 5867387 - 1 8 chr18 5859083 5866832 + 1 9 chr20 1213189 1221186 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9185465 | 9194572 | a | 0 | + | | chr1 | 166102 | 171790 | a | 0 | + | | chr1 | 6923754 | 6933170 | a | 0 | + | | chr1 | 792177 | 802176 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr10 | 3638745 | 3647100 | a | 0 | + | | chr12 | 3750546 | 3755166 | a | 0 | - | | chr14 | 2328145 | 2329080 | a | 0 | - | | chr17 | 46439 | 51343 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp6bgc7vzg/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 166102 171790 + 1 chr1 792177 802176 + 1 chr1 1359836 1360390 - 1 chr1 4512199 4519797 + 1 chr1 6923754 6933170 + 1 chr1 7021852 7024904 - 1 chr1 9185465 9194572 + 1 chr10 3638745 3647100 + 1 chr12 3750546 3755166 - 1 chr14 2328145 2329080 - 1 chr17 46439 51343 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 166102 171790 + 1 1 chr1 792177 802176 + 1 2 chr1 1359836 1360390 - 1 3 chr1 4512199 4519797 + 1 4 chr1 6923754 6933170 + 1 5 chr1 7021852 7024904 - 1 6 chr1 9185465 9194572 + 1 7 chr10 3638745 3647100 + 1 8 chr12 3750546 3755166 - 1 9 chr14 2328145 2329080 - 1 10 chr17 46439 51343 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4769879 | 4776097 | a | 0 | + | | chr1 | 2632664 | 2642184 | a | 0 | - | | chr1 | 3853588 | 3860091 | a | 0 | - | | chr1 | 6878281 | 6880942 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr16 | 6286278 | 6290997 | a | 0 | - | | chr16 | 4563810 | 4573242 | a | 0 | - | | chrM | 5761620 | 5763123 | a | 0 | - | | chrX | 6690667 | 6699464 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmphbqq9sc5/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2632664 2642184 - 1 chr1 3853588 3860091 - 1 chr1 4769879 4776097 + 1 chr1 6878281 6880942 - 1 chr1 7322450 7326404 - 1 chr13 10000000 10005994 + 1 chr14 4693958 4702404 - 1 chr16 4563810 4573242 - 1 chr16 6286278 6290997 - 1 chrM 5761620 5763123 - 1 chrX 6690667 6699464 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 2632664 2642184 - 1 1 chr1 3853588 3860091 - 1 2 chr1 4769879 4776097 + 1 3 chr1 6878281 6880942 - 1 4 chr1 7322450 7326404 - 1 5 chr13 10000000 10005994 + 1 6 chr14 4693958 4702404 - 1 7 chr16 4563810 4573242 - 1 8 chr16 6286278 6290997 - 1 9 chrM 5761620 5763123 - 1 10 chrX 6690667 6699464 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5860120 | 5864718 | a | 0 | + | | chr1 | 8268553 | 8272843 | a | 0 | + | | chr1 | 8268301 | 8272303 | a | 0 | + | | chr1 | 8817502 | 8817904 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr4 | 570436 | 576346 | a | 0 | + | | chr4 | 9756041 | 9763463 | a | 0 | + | | chr4 | 8764076 | 8771907 | a | 0 | - | | chr11 | 7030580 | 7037810 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp7iljlb3q/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 3825373 3831283 + 1 chr1 5860120 5864718 + 1 chr1 8268301 8272843 + 2 chr1 8817502 8817904 + 1 chr1 9880568 9887467 - 1 chr11 7030580 7037810 + 1 chr4 570436 576346 + 1 chr4 8764076 8771907 - 1 chr4 9756041 9763463 + 1 chrM 9446969 9453048 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 3825373 3831283 + 1 1 chr1 5860120 5864718 + 1 2 chr1 8268301 8272843 + 2 3 chr1 8817502 8817904 + 1 4 chr1 9880568 9887467 - 1 5 chr11 7030580 7037810 + 1 6 chr4 570436 576346 + 1 7 chr4 8764076 8771907 - 1 8 chr4 9756041 9763463 + 1 9 chrM 9446969 9453048 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 772653 | 775847 | a | 0 | - | | chr1 | 2393216 | 2396105 | a | 0 | - | | chr1 | 8288843 | 8294279 | a | 0 | - | | chr2 | 9105210 | 9108404 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr5 | 2356413 | 2364669 | a | 0 | - | | chr15 | 7876998 | 7882302 | a | 0 | + | | chr20 | 469970 | 476501 | a | 0 | - | | chrY | 1911545 | 1911963 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 9 rows and 6 columns from 7 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpd32jh5vn/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 772653 775847 - 1 chr1 2393216 2396105 - 1 chr1 8288843 8294279 - 1 chr15 7876998 7882302 + 1 chr2 9105210 9108404 - 1 chr20 469970 476501 - 1 chr3 5875041 5878261 - 1 chr5 2356413 2364669 - 1 chrY 1911545 1911963 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 772653 775847 - 1 1 chr1 2393216 2396105 - 1 2 chr1 8288843 8294279 - 1 3 chr15 7876998 7882302 + 1 4 chr2 9105210 9108404 - 1 5 chr20 469970 476501 - 1 6 chr3 5875041 5878261 - 1 7 chr5 2356413 2364669 - 1 8 chrY 1911545 1911963 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6247434 | 6257407 | a | 0 | + | | chr1 | 5872408 | 5882381 | a | 0 | + | | chr1 | 6030807 | 6040780 | a | 0 | + | | chr1 | 8374714 | 8384687 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr6 | 4180726 | 4190699 | a | 0 | - | | chr7 | 8563168 | 8573141 | a | 0 | - | | chr13 | 4883285 | 4893258 | a | 0 | - | | chr21 | 4546981 | 4556954 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpwcopyr2s/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 5872408 5882381 + 1 chr1 6030807 6040780 + 1 chr1 6247434 6257407 + 1 chr1 8374714 8384687 - 1 chr1 8571633 8575962 - 1 chr13 4883285 4893258 - 1 chr21 4546981 4556954 + 1 chr4 2428890 2438863 - 1 chr4 8296033 8306006 - 1 chr6 4180726 4190699 - 1 chr7 8563168 8573141 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 5872408 5882381 + 1 1 chr1 6030807 6040780 + 1 2 chr1 6247434 6257407 + 1 3 chr1 8374714 8384687 - 1 4 chr1 8571633 8575962 - 1 5 chr13 4883285 4893258 - 1 6 chr21 4546981 4556954 + 1 7 chr4 2428890 2438863 - 1 8 chr4 8296033 8306006 - 1 9 chr6 4180726 4190699 - 1 10 chr7 8563168 8573141 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5068213 | 5077990 | a | 0 | - | | chr4 | 5918043 | 5928042 | a | 0 | + | | chr4 | 760273 | 761776 | a | 0 | - | | chr5 | 7863645 | 7872177 | a | 0 | - | | chr14 | 2335754 | 2337962 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpiu7z_lg7/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 5068213 5077990 - 1 chr14 2335754 2337962 + 1 chr4 760273 761776 - 1 chr4 5918043 5928042 + 1 chr5 7863645 7872177 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 5068213 5077990 - 1 1 chr14 2335754 2337962 + 1 2 chr4 760273 761776 - 1 3 chr4 5918043 5928042 + 1 4 chr5 7863645 7872177 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3028881 | 3038880 | a | 0 | + | | chr1 | 5304669 | 5314668 | a | 0 | - | | chr1 | 3850095 | 3860094 | a | 0 | - | | chr6 | 3850095 | 3860094 | a | 0 | + | | chr9 | 2497905 | 2507904 | a | 0 | + | | chr12 | 3865445 | 3875444 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmphzrccfe6/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 3028881 3038880 + 1 chr1 3850095 3860094 - 1 chr1 5304669 5314668 - 1 chr12 3865445 3875444 + 1 chr6 3850095 3860094 + 1 chr9 2497905 2507904 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 3028881 3038880 + 1 1 chr1 3850095 3860094 - 1 2 chr1 5304669 5314668 - 1 3 chr12 3865445 3875444 + 1 4 chr6 3850095 3860094 + 1 5 chr9 2497905 2507904 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6581467 | 6587562 | a | 0 | + | | chr1 | 6691607 | 6697702 | a | 0 | + | | chr1 | 5340780 | 5346875 | a | 0 | + | | chr1 | 1022340 | 1027612 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr1 | 9011987 | 9011988 | a | 0 | - | | chr1 | 1986282 | 1992377 | a | 0 | - | | chr1 | 696343 | 705466 | a | 0 | - | | chr1 | 4290716 | 4299508 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpir32pwgj/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 696343 705466 - 1 chr1 1022340 1027612 - 1 chr1 1986282 1992377 - 1 chr1 4290716 4299508 - 1 chr1 5340780 5346875 + 1 chr1 6581467 6587562 + 1 chr1 6691607 6697702 + 1 chr1 9011987 9011988 - 1 chr11 6912724 6918819 + 1 chr17 8861303 8867398 + 1 chr6 4001183 4005761 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 696343 705466 - 1 1 chr1 1022340 1027612 - 1 2 chr1 1986282 1992377 - 1 3 chr1 4290716 4299508 - 1 4 chr1 5340780 5346875 + 1 5 chr1 6581467 6587562 + 1 6 chr1 6691607 6697702 + 1 7 chr1 9011987 9011988 - 1 8 chr11 6912724 6918819 + 1 9 chr17 8861303 8867398 + 1 10 chr6 4001183 4005761 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2 | 2875 | a | 0 | + | | chr1 | 2499146 | 2499590 | a | 0 | + | | chr1 | 2379681 | 2386592 | a | 0 | + | | chr2 | 2344394 | 2348853 | a | 0 | + | | chr2 | 1011879 | 1017427 | a | 0 | - | | chr12 | 4743030 | 4752491 | a | 0 | - | | chrM | 9830976 | 9833436 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 7 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpayvzu_xc/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2 2875 + 1 chr1 2379681 2386592 + 1 chr1 2499146 2499590 + 1 chr12 4743030 4752491 - 1 chr2 1011879 1017427 - 1 chr2 2344394 2348853 + 1 chrM 9830976 9833436 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 2 2875 + 1 1 chr1 2379681 2386592 + 1 2 chr1 2499146 2499590 + 1 3 chr12 4743030 4752491 - 1 4 chr2 1011879 1017427 - 1 5 chr2 2344394 2348853 + 1 6 chrM 9830976 9833436 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4967798 | 4973996 | a | 0 | + | | chr1 | 8858287 | 8860084 | a | 0 | + | | chr1 | 7858841 | 7865669 | a | 0 | + | | chr1 | 1524656 | 1525871 | a | 0 | - | | chr1 | 6880934 | 6882950 | a | 0 | - | | chr8 | 5343360 | 5345864 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpunfqakox/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1524656 1525871 - 1 chr1 4967798 4973996 + 1 chr1 6880934 6882950 - 1 chr1 7858841 7865669 + 1 chr1 8858287 8860084 + 1 chr8 5343360 5345864 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1524656 1525871 - 1 1 chr1 4967798 4973996 + 1 2 chr1 6880934 6882950 - 1 3 chr1 7858841 7865669 + 1 4 chr1 8858287 8860084 + 1 5 chr8 5343360 5345864 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2895960 | 2902387 | a | 0 | + | | chr1 | 2379419 | 2387158 | a | 0 | + | | chr1 | 9861450 | 9865423 | a | 0 | + | | chr1 | 5726037 | 5732226 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chrM | 7561112 | 7567083 | a | 0 | + | | chrM | 452219 | 456397 | a | 0 | + | | chrM | 8457959 | 8466399 | a | 0 | + | | chrM | 8230108 | 8230787 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp43b85tpe/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2379419 2387158 + 1 chr1 2895960 2902387 + 1 chr1 5726037 5732226 + 1 chr1 9861450 9865423 + 1 chr2 3627362 3627364 + 1 chrM 452219 456397 + 1 chrM 893230 901375 + 1 chrM 7561112 7567083 + 1 chrM 8230108 8230787 + 1 chrM 8457959 8466399 + 1 chrX 6641174 6641335 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 2379419 2387158 + 1 1 chr1 2895960 2902387 + 1 2 chr1 5726037 5732226 + 1 3 chr1 9861450 9865423 + 1 4 chr2 3627362 3627364 + 1 5 chrM 452219 456397 + 1 6 chrM 893230 901375 + 1 7 chrM 7561112 7567083 + 1 8 chrM 8230108 8230787 + 1 9 chrM 8457959 8466399 + 1 10 chrX 6641174 6641335 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9304796 | 9310422 | a | 0 | + | | chr1 | 9304796 | 9314309 | a | 0 | + | | chr1 | 9304796 | 9308906 | a | 0 | - | | chr11 | 9304796 | 9309691 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpyv69ds_e/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 9304796 9308906 - 1 chr1 9304796 9314309 + 2 chr11 9304796 9309691 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 9304796 9308906 - 1 1 chr1 9304796 9314309 + 2 2 chr11 9304796 9309691 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 75361 | 80590 | a | 0 | + | | chr1 | 5929167 | 5935554 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpz0y9x4sv/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 75361 80590 + 1 chr1 5929167 5935554 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 75361 80590 + 1 1 chr1 5929167 5935554 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3568718 | 3573053 | a | 0 | - | | chr1 | 1074201 | 1078001 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp999c2qey/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1074201 1078001 - 1 chr1 3568718 3573053 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1074201 1078001 - 1 1 chr1 3568718 3573053 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9545857 | 9552997 | a | 0 | + | | chr1 | 6429301 | 6437691 | a | 0 | - | | chr3 | 6164029 | 6169120 | a | 0 | + | | chr11 | 10000000 | 10008384 | a | 0 | + | | chr11 | 4087262 | 4089237 | a | 0 | - | | chrX | 4441907 | 4449727 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp_xb6d9a7/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 6429301 6437691 - 1 chr1 9545857 9552997 + 1 chr11 4087262 4089237 - 1 chr11 10000000 10008384 + 1 chr3 6164029 6169120 + 1 chrX 4441907 4449727 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 6429301 6437691 - 1 1 chr1 9545857 9552997 + 1 2 chr11 4087262 4089237 - 1 3 chr11 10000000 10008384 + 1 4 chr3 6164029 6169120 + 1 5 chrX 4441907 4449727 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 798871 | 802158 | a | 0 | - | | chr3 | 6657644 | 6660259 | a | 0 | + | | chr14 | 2821777 | 2826527 | a | 0 | + | | chr16 | 3971077 | 3972802 | a | 0 | - | | chr20 | 3822050 | 3823299 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpfeafl_jk/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 798871 802158 - 1 chr14 2821777 2826527 + 1 chr16 3971077 3972802 - 1 chr20 3822050 3823299 - 1 chr3 6657644 6660259 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 798871 802158 - 1 1 chr14 2821777 2826527 + 1 2 chr16 3971077 3972802 - 1 3 chr20 3822050 3823299 - 1 4 chr3 6657644 6660259 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 449630 | 450958 | a | 0 | - | | chr1 | 449630 | 454247 | a | 0 | - | | chr4 | 4470757 | 4474811 | a | 0 | + | | chr5 | 449630 | 450408 | a | 0 | + | | chr9 | 449630 | 456325 | a | 0 | - | | chr15 | 449630 | 455448 | a | 0 | - | | chr20 | 5191304 | 5194292 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 7 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpg8_7fcrb/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 449630 454247 - 2 chr15 449630 455448 - 1 chr20 5191304 5194292 - 1 chr4 4470757 4474811 + 1 chr5 449630 450408 + 1 chr9 449630 456325 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 449630 454247 - 2 1 chr15 449630 455448 - 1 2 chr20 5191304 5194292 - 1 3 chr4 4470757 4474811 + 1 4 chr5 449630 450408 + 1 5 chr9 449630 456325 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3818576 | 3820484 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpscelax0g/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 3818576 3820484 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 3818576 3820484 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 925642 | 926444 | a | 0 | - | | chrX | 1465101 | 1473072 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpvcjst63i/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 925642 926444 - 1 chrX 1465101 1473072 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 925642 926444 - 1 1 chrX 1465101 1473072 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6141934 | 6143782 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmplnyagmuf/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 6141934 6143782 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 6141934 6143782 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5866352 | 5867272 | a | 0 | + | | chr3 | 5037404 | 5044968 | a | 0 | - | | chr3 | 8458295 | 8467374 | a | 0 | - | | chr6 | 6711931 | 6712786 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpm933v5l9/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 5866352 5867272 + 1 chr3 5037404 5044968 - 1 chr3 8458295 8467374 - 1 chr6 6711931 6712786 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 5866352 5867272 + 1 1 chr3 5037404 5044968 - 1 2 chr3 8458295 8467374 - 1 3 chr6 6711931 6712786 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 9410 | a | 0 | + | | chr1 | 4286999 | 4293282 | a | 0 | + | | chr1 | 9497976 | 9503544 | a | 0 | - | | chr3 | 4254097 | 4260247 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr20 | 8153755 | 8155347 | a | 0 | + | | chr22 | 8963319 | 8970955 | a | 0 | + | | chrX | 136928 | 142976 | a | 0 | + | | chrY | 6013210 | 6020475 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 9 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpgtvcgni4/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 9410 + 1 chr1 4286999 4293282 + 1 chr1 9497976 9503544 - 1 chr12 158164 168150 + 1 chr15 820198 826293 + 1 chr20 8153755 8155347 + 1 chr22 8963319 8970955 + 1 chr3 4254097 4260247 + 1 chr8 7399649 7404917 - 1 chrX 136928 142976 + 1 chrY 6013210 6020475 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1 9410 + 1 1 chr1 4286999 4293282 + 1 2 chr1 9497976 9503544 - 1 3 chr12 158164 168150 + 1 4 chr15 820198 826293 + 1 5 chr20 8153755 8155347 + 1 6 chr22 8963319 8970955 + 1 7 chr3 4254097 4260247 + 1 8 chr8 7399649 7404917 - 1 9 chrX 136928 142976 + 1 10 chrY 6013210 6020475 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3876446 | 3881885 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpp5gu5ekg/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 3876446 3881885 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 3876446 3881885 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8938552 | 8940344 | a | 0 | + | | chr13 | 9775865 | 9777458 | a | 0 | + | | chrX | 9010962 | 9012584 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpf8prudml/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 8938552 8940344 + 1 chr13 9775865 9777458 + 1 chrX 9010962 9012584 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 8938552 8940344 + 1 1 chr13 9775865 9777458 + 1 2 chrX 9010962 9012584 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr16 | 3468334 | 3471663 | a | 0 | + | | chr16 | 8263527 | 8272204 | a | 0 | - | | chr16 | 4549311 | 4549928 | a | 0 | - | | chr16 | 6859754 | 6865043 | a | 0 | - | | chr16 | 8579067 | 8584760 | a | 0 | - | | chr16 | 3189544 | 3192577 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp6t2zewsy/f1.bed) resultresultresultresultresultresultresultresultresultresult chr16 3189544 3192577 - 1 chr16 3468334 3471663 + 1 chr16 4549311 4549928 - 1 chr16 6859754 6865043 - 1 chr16 8263527 8272204 - 1 chr16 8579067 8584760 - 1 bedtools_df Chromosome Start End Strand Count 0 chr16 3189544 3192577 - 1 1 chr16 3468334 3471663 + 1 2 chr16 4549311 4549928 - 1 3 chr16 6859754 6865043 - 1 4 chr16 8263527 8272204 - 1 5 chr16 8579067 8584760 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3682735 | 3686658 | a | 0 | + | | chr1 | 2765715 | 2768203 | a | 0 | + | | chr1 | 1 | 226 | a | 0 | - | | chr1 | 2906345 | 2906570 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpn_smuhtt/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 226 - 1 chr1 2765715 2768203 + 1 chr1 2906345 2906570 - 1 chr1 3682735 3686658 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1 226 - 1 1 chr1 2765715 2768203 + 1 2 chr1 2906345 2906570 - 1 3 chr1 3682735 3686658 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1933190 | 1938630 | a | 0 | + | | chr1 | 2864702 | 2870142 | a | 0 | + | | chr1 | 3340657 | 3346097 | a | 0 | - | | chr1 | 7050778 | 7056218 | a | 0 | - | | chr6 | 8212458 | 8219227 | a | 0 | - | | chr13 | 3115929 | 3121369 | a | 0 | - | | chr22 | 1475795 | 1480434 | a | 0 | - | | chr22 | 3231604 | 3240565 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 8 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpyvl9n11c/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1933190 1938630 + 1 chr1 2864702 2870142 + 1 chr1 3340657 3346097 - 1 chr1 7050778 7056218 - 1 chr13 3115929 3121369 - 1 chr22 1475795 1480434 - 1 chr22 3231604 3240565 - 1 chr6 8212458 8219227 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1933190 1938630 + 1 1 chr1 2864702 2870142 + 1 2 chr1 3340657 3346097 - 1 3 chr1 7050778 7056218 - 1 4 chr13 3115929 3121369 - 1 5 chr22 1475795 1480434 - 1 6 chr22 3231604 3240565 - 1 7 chr6 8212458 8219227 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7978618 | 7983161 | a | 0 | + | | chr1 | 10000000 | 10004237 | a | 0 | + | | chr1 | 6294816 | 6296127 | a | 0 | + | | chr1 | 6739439 | 6740923 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr18 | 8836884 | 8838193 | a | 0 | - | | chr21 | 9949062 | 9953466 | a | 0 | + | | chrM | 7058852 | 7063008 | a | 0 | + | | chrY | 870029 | 874582 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpqmv3bxuw/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 458668 460139 - 1 chr1 544647 546825 - 1 chr1 6294816 6296127 + 1 chr1 6739439 6740923 - 1 chr1 7978618 7983161 + 1 chr1 10000000 10004237 + 1 chr10 7814144 7820271 + 1 chr18 8836884 8838193 - 1 chr21 9949062 9953466 + 1 chrM 7058852 7063008 + 1 chrY 870029 874582 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 458668 460139 - 1 1 chr1 544647 546825 - 1 2 chr1 6294816 6296127 + 1 3 chr1 6739439 6740923 - 1 4 chr1 7978618 7983161 + 1 5 chr1 10000000 10004237 + 1 6 chr10 7814144 7820271 + 1 7 chr18 8836884 8838193 - 1 8 chr21 9949062 9953466 + 1 9 chrM 7058852 7063008 + 1 10 chrY 870029 874582 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3621712 | 3627561 | a | 0 | + | | chr1 | 7764297 | 7766140 | a | 0 | + | | chr7 | 3621712 | 3623555 | a | 0 | - | | chr12 | 7359148 | 7362590 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp6uojea1h/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 3621712 3627561 + 1 chr1 7764297 7766140 + 1 chr12 7359148 7362590 + 1 chr7 3621712 3623555 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 3621712 3627561 + 1 1 chr1 7764297 7766140 + 1 2 chr12 7359148 7362590 + 1 3 chr7 3621712 3623555 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr20 | 3676233 | 3678813 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpt2ojw4g6/f1.bed) resultresultresultresultresultresultresultresultresultresult chr20 3676233 3678813 + 1 bedtools_df Chromosome Start End Strand Count 0 chr20 3676233 3678813 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4042345 | 4044559 | a | 0 | - | | chr14 | 9656597 | 9666317 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpu6gdziwg/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 4042345 4044559 - 1 chr14 9656597 9666317 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 4042345 4044559 - 1 1 chr14 9656597 9666317 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6537232 | 6546911 | a | 0 | + | | chrM | 2351493 | 2358296 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpuepbilcd/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 6537232 6546911 + 1 chrM 2351493 2358296 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 6537232 6546911 + 1 1 chrM 2351493 2358296 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5573746 | 5577594 | a | 0 | + | | chr1 | 7495610 | 7502903 | a | 0 | + | | chr1 | 4586208 | 4592759 | a | 0 | + | | chr1 | 1964383 | 1969403 | a | 0 | + | | chr1 | 9690168 | 9699119 | a | 0 | + | | chr17 | 7346014 | 7350285 | a | 0 | + | | chr18 | 8051840 | 8056263 | a | 0 | + | | chrM | 6946237 | 6950353 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 8 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpqafa5iar/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1964383 1969403 + 1 chr1 4586208 4592759 + 1 chr1 5573746 5577594 + 1 chr1 7495610 7502903 + 1 chr1 9690168 9699119 + 1 chr17 7346014 7350285 + 1 chr18 8051840 8056263 + 1 chrM 6946237 6950353 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1964383 1969403 + 1 1 chr1 4586208 4592759 + 1 2 chr1 5573746 5577594 + 1 3 chr1 7495610 7502903 + 1 4 chr1 9690168 9699119 + 1 5 chr17 7346014 7350285 + 1 6 chr18 8051840 8056263 + 1 7 chrM 6946237 6950353 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 203668 | 208684 | a | 0 | + | | chr10 | 9856328 | 9861659 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpyeemzj5d/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 203668 208684 + 1 chr10 9856328 9861659 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 203668 208684 + 1 1 chr10 9856328 9861659 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2252026 | 2258885 | a | 0 | + | | chr1 | 9486374 | 9496247 | a | 0 | - | | chr1 | 2596751 | 2605737 | a | 0 | - | | chr1 | 4348383 | 4354451 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr13 | 1828822 | 1833614 | a | 0 | + | | chr17 | 8647743 | 8648639 | a | 0 | + | | chr22 | 9999999 | 10005272 | a | 0 | + | | chrX | 5024707 | 5034669 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 7 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpul38cw6_/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1174167 1179510 - 1 chr1 2252026 2258885 + 1 chr1 2596751 2605737 - 1 chr1 4348383 4354451 - 1 chr1 9486374 9496247 - 1 chr13 1828822 1833614 + 1 chr17 8647743 8648639 + 1 chr22 9999999 10005272 + 1 chr3 733070 738979 - 1 chr4 9722390 9731691 - 1 chrX 5024707 5034669 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1174167 1179510 - 1 1 chr1 2252026 2258885 + 1 2 chr1 2596751 2605737 - 1 3 chr1 4348383 4354451 - 1 4 chr1 9486374 9496247 - 1 5 chr13 1828822 1833614 + 1 6 chr17 8647743 8648639 + 1 7 chr22 9999999 10005272 + 1 8 chr3 733070 738979 - 1 9 chr4 9722390 9731691 - 1 10 chrX 5024707 5034669 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 989383 | 998596 | a | 0 | + | | chr1 | 3155934 | 3160809 | a | 0 | - | | chr1 | 2533707 | 2540429 | a | 0 | - | | chr1 | 9785365 | 9793645 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr7 | 9999999 | 10005715 | a | 0 | + | | chr7 | 6877367 | 6879854 | a | 0 | + | | chr9 | 5916240 | 5917631 | a | 0 | + | | chr9 | 1671452 | 1679611 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 9 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmps9_qlg7o/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 989383 998596 + 1 chr1 2533707 2540429 - 1 chr1 3155934 3160809 - 1 chr1 9785365 9793645 - 1 chr12 8536602 8539565 + 1 chr7 6877367 6879854 + 1 chr7 9999999 10005715 + 1 chr9 1671452 1679611 - 1 chr9 5916240 5917631 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 989383 998596 + 1 1 chr1 2533707 2540429 - 1 2 chr1 3155934 3160809 - 1 3 chr1 9785365 9793645 - 1 4 chr12 8536602 8539565 + 1 5 chr7 6877367 6879854 + 1 6 chr7 9999999 10005715 + 1 7 chr9 1671452 1679611 - 1 8 chr9 5916240 5917631 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6786964 | 6793612 | a | 0 | + | | chr1 | 3633224 | 3636273 | a | 0 | + | | chr1 | 182387 | 189035 | a | 0 | - | | chr1 | 7151009 | 7153530 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr5 | 6102277 | 6105148 | a | 0 | + | | chr9 | 9278844 | 9285492 | a | 0 | + | | chr15 | 9999999 | 10002176 | a | 0 | - | | chr20 | 9278844 | 9286108 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpz26jbu79/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 182387 189035 - 1 chr1 3633224 3636273 + 1 chr1 3744833 3749842 - 1 chr1 5351940 5358163 - 1 chr1 6786964 6793612 + 1 chr1 7151009 7153530 - 1 chr1 9278844 9285492 - 1 chr15 9999999 10002176 - 1 chr20 9278844 9286108 - 1 chr5 6102277 6105148 + 1 chr9 9278844 9285492 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 182387 189035 - 1 1 chr1 3633224 3636273 + 1 2 chr1 3744833 3749842 - 1 3 chr1 5351940 5358163 - 1 4 chr1 6786964 6793612 + 1 5 chr1 7151009 7153530 - 1 6 chr1 9278844 9285492 - 1 7 chr15 9999999 10002176 - 1 8 chr20 9278844 9286108 - 1 9 chr5 6102277 6105148 + 1 10 chr9 9278844 9285492 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4050929 | 4051492 | a | 0 | + | | chr20 | 1172830 | 1177505 | a | 0 | + | | chr20 | 8463410 | 8464762 | a | 0 | + | | chr20 | 4050929 | 4055711 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpc9x6sqm6/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 4050929 4051492 + 1 chr20 1172830 1177505 + 1 chr20 4050929 4055711 - 1 chr20 8463410 8464762 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 4050929 4051492 + 1 1 chr20 1172830 1177505 + 1 2 chr20 4050929 4055711 - 1 3 chr20 8463410 8464762 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9808541 | 9814250 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmphcg73b5_/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 9808541 9814250 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 9808541 9814250 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1057982 | 1062567 | a | 0 | + | | chr1 | 1381904 | 1388566 | a | 0 | + | | chr1 | 9302119 | 9308198 | a | 0 | + | | chr1 | 6684932 | 6688198 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr6 | 5480709 | 5488407 | a | 0 | + | | chr6 | 2601256 | 2605815 | a | 0 | - | | chr15 | 7199197 | 7200465 | a | 0 | + | | chrM | 4741878 | 4751878 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp0ynfq_xo/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1057982 1062567 + 1 chr1 1381904 1388566 + 1 chr1 2791442 2797393 + 1 chr1 6684932 6688198 + 1 chr1 9302119 9308198 + 1 chr15 7199197 7200465 + 1 chr4 6429201 6430171 + 1 chr6 2601256 2605815 - 1 chr6 5480709 5488407 + 1 chrM 4741878 4751878 + 1 chrY 10000000 10005197 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1057982 1062567 + 1 1 chr1 1381904 1388566 + 1 2 chr1 2791442 2797393 + 1 3 chr1 6684932 6688198 + 1 4 chr1 9302119 9308198 + 1 5 chr15 7199197 7200465 + 1 6 chr4 6429201 6430171 + 1 7 chr6 2601256 2605815 - 1 8 chr6 5480709 5488407 + 1 9 chrM 4741878 4751878 + 1 10 chrY 10000000 10005197 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8236778 | 8245861 | a | 0 | + | | chr1 | 8786531 | 8793109 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmphxhvrk5a/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 8236778 8245861 + 1 chr1 8786531 8793109 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 8236778 8245861 + 1 1 chr1 8786531 8793109 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8686076 | 8690559 | a | 0 | + | | chr1 | 680970 | 689172 | a | 0 | + | | chr1 | 8686076 | 8691229 | a | 0 | - | | chr6 | 8686076 | 8687725 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp1mkwnour/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 680970 689172 + 1 chr1 8686076 8690559 + 1 chr1 8686076 8691229 - 1 chr6 8686076 8687725 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 680970 689172 + 1 1 chr1 8686076 8690559 + 1 2 chr1 8686076 8691229 - 1 3 chr6 8686076 8687725 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9478300 | 9481666 | a | 0 | + | | chr1 | 5918940 | 5921619 | a | 0 | + | | chr1 | 1485147 | 1494351 | a | 0 | - | | chr1 | 4668022 | 4674924 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr11 | 4471279 | 4478089 | a | 0 | - | | chr12 | 9985435 | 9993242 | a | 0 | + | | chr16 | 4849223 | 4853302 | a | 0 | + | | chr21 | 6418232 | 6418376 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpbr3qpd17/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1485147 1494351 - 1 chr1 2974971 2978019 - 1 chr1 4668022 4674924 - 1 chr1 5918940 5921619 + 1 chr1 7434462 7435303 - 1 chr1 9478300 9481666 + 1 chr10 7560359 7563635 + 1 chr11 4471279 4478089 - 1 chr12 9985435 9993242 + 1 chr16 4849223 4853302 + 1 chr21 6418232 6418376 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1485147 1494351 - 1 1 chr1 2974971 2978019 - 1 2 chr1 4668022 4674924 - 1 3 chr1 5918940 5921619 + 1 4 chr1 7434462 7435303 - 1 5 chr1 9478300 9481666 + 1 6 chr10 7560359 7563635 + 1 7 chr11 4471279 4478089 - 1 8 chr12 9985435 9993242 + 1 9 chr16 4849223 4853302 + 1 10 chr21 6418232 6418376 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1850261 | 1854791 | a | 0 | + | | chr1 | 1483773 | 1485355 | a | 0 | - | | chr1 | 1483773 | 1487925 | a | 0 | - | | chr1 | 1483773 | 1485009 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr1 | 1483773 | 1485009 | a | 0 | - | | chr1 | 2937505 | 2945675 | a | 0 | - | | chr1 | 1483773 | 1488478 | a | 0 | - | | chr1 | 1483773 | 1492459 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 10 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpzkvjq7rv/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1483773 1492459 - 5 chr1 1850261 1854791 + 1 chr1 2937505 2945675 - 1 chr2 1483773 1484744 + 1 chr21 1483773 1485864 - 1 chrM 1483773 1484163 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1483773 1492459 - 5 1 chr1 1850261 1854791 + 1 2 chr1 2937505 2945675 - 1 3 chr2 1483773 1484744 + 1 4 chr21 1483773 1485864 - 1 5 chrM 1483773 1484163 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5401981 | 5406519 | a | 0 | - | | chr1 | 5401981 | 5403261 | a | 0 | - | | chr5 | 1363856 | 1366865 | a | 0 | + | | chr17 | 6495317 | 6497636 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmppymzl52c/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 5401981 5406519 - 2 chr17 6495317 6497636 - 1 chr5 1363856 1366865 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 5401981 5406519 - 2 1 chr17 6495317 6497636 - 1 2 chr5 1363856 1366865 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr7 | 5811392 | 5818615 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpi_u_h7ze/f1.bed) resultresultresultresultresultresultresultresultresultresult chr7 5811392 5818615 + 1 bedtools_df Chromosome Start End Strand Count 0 chr7 5811392 5818615 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6109307 | 6119242 | a | 0 | - | | chr1 | 4374306 | 4383725 | a | 0 | - | | chr1 | 6109307 | 6115885 | a | 0 | - | | chr3 | 6109307 | 6114969 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr8 | 6109307 | 6118508 | a | 0 | + | | chr8 | 9409937 | 9419937 | a | 0 | + | | chr19 | 6359337 | 6360375 | a | 0 | - | | chr21 | 6109307 | 6110335 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 9 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpoqflri93/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 4374306 4383725 - 1 chr1 6109307 6119242 - 2 chr19 6359337 6360375 - 1 chr21 6109307 6110335 - 1 chr3 6109307 6114969 - 1 chr8 6109307 6118508 + 1 chr8 9409937 9419937 + 1 chrY 6109307 6114536 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 4374306 4383725 - 1 1 chr1 6109307 6119242 - 2 2 chr19 6359337 6360375 - 1 3 chr21 6109307 6110335 - 1 4 chr3 6109307 6114969 - 1 5 chr8 6109307 6118508 + 1 6 chr8 9409937 9419937 + 1 7 chrY 6109307 6114536 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6299314 | 6302971 | a | 0 | - | | chr1 | 6224938 | 6227322 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp82stv299/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 6224938 6227322 - 1 chr1 6299314 6302971 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 6224938 6227322 - 1 1 chr1 6299314 6302971 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1037278 | 1037280 | a | 0 | + | | chr1 | 3160902 | 3160904 | a | 0 | - | | chr1 | 7694454 | 7696051 | a | 0 | - | | chr1 | 1037278 | 1039192 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr2 | 1037278 | 1037280 | a | 0 | - | | chr8 | 7367590 | 7367592 | a | 0 | - | | chr10 | 4374868 | 4374870 | a | 0 | - | | chr17 | 2487469 | 2487471 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 10 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpyok5ikfk/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2853 - 1 chr1 1037278 1037280 + 1 chr1 1037278 1039192 - 2 chr1 3160902 3160904 - 1 chr1 7694454 7696051 - 1 chr10 4374868 4374870 - 1 chr17 2487469 2487471 - 1 chr2 1037278 1037280 - 1 chr8 7367590 7367592 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1 2853 - 1 1 chr1 1037278 1037280 + 1 2 chr1 1037278 1039192 - 2 3 chr1 3160902 3160904 - 1 4 chr1 7694454 7696051 - 1 5 chr10 4374868 4374870 - 1 6 chr17 2487469 2487471 - 1 7 chr2 1037278 1037280 - 1 8 chr8 7367590 7367592 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6544903 | 6550585 | a | 0 | - | | chr2 | 5620707 | 5626389 | a | 0 | + | | chr4 | 874951 | 880633 | a | 0 | - | | chr8 | 9234186 | 9236889 | a | 0 | + | | chr18 | 5236277 | 5241185 | a | 0 | + | | chr18 | 3734552 | 3740234 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpzj_q0xw9/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 6544903 6550585 - 1 chr18 3734552 3740234 - 1 chr18 5236277 5241185 + 1 chr2 5620707 5626389 + 1 chr4 874951 880633 - 1 chr8 9234186 9236889 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 6544903 6550585 - 1 1 chr18 3734552 3740234 - 1 2 chr18 5236277 5241185 + 1 3 chr2 5620707 5626389 + 1 4 chr4 874951 880633 - 1 5 chr8 9234186 9236889 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2653786 | 2654698 | a | 0 | + | | chr1 | 9333989 | 9335855 | a | 0 | + | | chr1 | 5714305 | 5716319 | a | 0 | + | | chr1 | 8438566 | 8447343 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr11 | 1232431 | 1239472 | a | 0 | - | | chr17 | 2710169 | 2712468 | a | 0 | - | | chr18 | 5437427 | 5443065 | a | 0 | - | | chrX | 5532416 | 5537436 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpyeipyh15/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2653786 2654698 + 1 chr1 5714305 5716319 + 1 chr1 6662144 6662238 - 1 chr1 8167710 8176889 - 1 chr1 8438566 8447343 - 1 chr1 9333989 9335855 + 1 chr11 1232431 1239472 - 1 chr17 2710169 2712468 - 1 chr18 5437427 5443065 - 1 chr6 1806872 1810061 - 1 chrX 5532416 5537436 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 2653786 2654698 + 1 1 chr1 5714305 5716319 + 1 2 chr1 6662144 6662238 - 1 3 chr1 8167710 8176889 - 1 4 chr1 8438566 8447343 - 1 5 chr1 9333989 9335855 + 1 6 chr11 1232431 1239472 - 1 7 chr17 2710169 2712468 - 1 8 chr18 5437427 5443065 - 1 9 chr6 1806872 1810061 - 1 10 chrX 5532416 5537436 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2579514 | 2586501 | a | 0 | + | | chr1 | 359438 | 368585 | a | 0 | + | | chr1 | 618085 | 622806 | a | 0 | + | | chr6 | 9411786 | 9416084 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp9zwq5ev8/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 359438 368585 + 1 chr1 618085 622806 + 1 chr1 2579514 2586501 + 1 chr6 9411786 9416084 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 359438 368585 + 1 1 chr1 618085 622806 + 1 2 chr1 2579514 2586501 + 1 3 chr6 9411786 9416084 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8514380 | 8519658 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpwp6km_sg/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 8514380 8519658 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 8514380 8519658 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2691164 | 2693542 | a | 0 | + | | chr1 | 7693991 | 7695259 | a | 0 | + | | chr1 | 9503227 | 9511097 | a | 0 | - | | chr1 | 9495066 | 9503584 | a | 0 | - | | chr9 | 6793872 | 6797335 | a | 0 | + | | chr11 | 3258044 | 3267817 | a | 0 | - | | chr22 | 5374310 | 5380929 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 7 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpw21oaewa/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2691164 2693542 + 1 chr1 7693991 7695259 + 1 chr1 9495066 9511097 - 2 chr11 3258044 3267817 - 1 chr22 5374310 5380929 + 1 chr9 6793872 6797335 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 2691164 2693542 + 1 1 chr1 7693991 7695259 + 1 2 chr1 9495066 9511097 - 2 3 chr11 3258044 3267817 - 1 4 chr22 5374310 5380929 + 1 5 chr9 6793872 6797335 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr22 | 1366860 | 1376357 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp_2dnqx6c/f1.bed) resultresultresultresultresultresultresultresultresultresult chr22 1366860 1376357 - 1 bedtools_df Chromosome Start End Strand Count 0 chr22 1366860 1376357 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 743021 | 746178 | a | 0 | + | | chr1 | 8522823 | 8529773 | a | 0 | + | | chr1 | 1401231 | 1401351 | a | 0 | - | | chr6 | 9362761 | 9369662 | a | 0 | + | | chr9 | 8792856 | 8801224 | a | 0 | + | | chr9 | 518302 | 518303 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmptnl16out/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 743021 746178 + 1 chr1 1401231 1401351 - 1 chr1 8522823 8529773 + 1 chr6 9362761 9369662 + 1 chr9 518302 518303 - 1 chr9 8792856 8801224 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 743021 746178 + 1 1 chr1 1401231 1401351 - 1 2 chr1 8522823 8529773 + 1 3 chr6 9362761 9369662 + 1 4 chr9 518302 518303 - 1 5 chr9 8792856 8801224 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6943599 | 6951744 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpiv8mykcs/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 6943599 6951744 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 6943599 6951744 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3951857 | 3959104 | a | 0 | + | | chr13 | 2034063 | 2038117 | a | 0 | - | | chr15 | 2234690 | 2237543 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp01cnq1pb/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 3951857 3959104 + 1 chr13 2034063 2038117 - 1 chr15 2234690 2237543 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 3951857 3959104 + 1 1 chr13 2034063 2038117 - 1 2 chr15 2234690 2237543 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9559901 | 9567618 | a | 0 | + | | chr5 | 8220286 | 8224985 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpnykn5biw/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 9559901 9567618 + 1 chr5 8220286 8224985 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 9559901 9567618 + 1 1 chr5 8220286 8224985 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3618524 | 3627690 | a | 0 | + | | chrX | 9079802 | 9081773 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp4p419x5y/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 3618524 3627690 + 1 chrX 9079802 9081773 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 3618524 3627690 + 1 1 chrX 9079802 9081773 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6726674 | 6731796 | a | 0 | - | | chr5 | 9469839 | 9472269 | a | 0 | - | | chr13 | 6318092 | 6323299 | a | 0 | + | | chr17 | 1286139 | 1291815 | a | 0 | - | | chr19 | 7313094 | 7318216 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp8tg80p3r/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 6726674 6731796 - 1 chr13 6318092 6323299 + 1 chr17 1286139 1291815 - 1 chr19 7313094 7318216 + 1 chr5 9469839 9472269 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 6726674 6731796 - 1 1 chr13 6318092 6323299 + 1 2 chr17 1286139 1291815 - 1 3 chr19 7313094 7318216 + 1 4 chr5 9469839 9472269 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4556157 | 4559860 | a | 0 | + | | chr7 | 3137441 | 3140173 | a | 0 | + | | chr8 | 3364886 | 3374885 | a | 0 | - | | chr18 | 5733537 | 5734796 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp4f2t1bpr/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 4556157 4559860 + 1 chr18 5733537 5734796 + 1 chr7 3137441 3140173 + 1 chr8 3364886 3374885 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 4556157 4559860 + 1 1 chr18 5733537 5734796 + 1 2 chr7 3137441 3140173 + 1 3 chr8 3364886 3374885 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3161954 | 3169694 | a | 0 | + | | chr1 | 4068982 | 4072643 | a | 0 | + | | chr1 | 2671806 | 2676390 | a | 0 | + | | chr1 | 2856102 | 2860086 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr1 | 3457854 | 3464129 | a | 0 | - | | chr1 | 3698394 | 3699885 | a | 0 | - | | chr1 | 4648987 | 4649503 | a | 0 | - | | chr1 | 9602429 | 9612227 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmplblcgyu8/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1600070 1606267 - 1 chr1 2671806 2676390 + 1 chr1 2856102 2860086 + 1 chr1 3161954 3169694 + 1 chr1 3457854 3464129 - 1 chr1 3698394 3699885 - 1 chr1 4068982 4072643 + 1 chr1 4648987 4649503 - 1 chr1 9602429 9612227 - 1 chr11 546360 548000 - 1 chrM 9999999 10007938 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1600070 1606267 - 1 1 chr1 2671806 2676390 + 1 2 chr1 2856102 2860086 + 1 3 chr1 3161954 3169694 + 1 4 chr1 3457854 3464129 - 1 5 chr1 3698394 3699885 - 1 6 chr1 4068982 4072643 + 1 7 chr1 4648987 4649503 - 1 8 chr1 9602429 9612227 - 1 9 chr11 546360 548000 - 1 10 chrM 9999999 10007938 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8775011 | 8777689 | a | 0 | + | | chr1 | 8775011 | 8785010 | a | 0 | - | | chr1 | 8775011 | 8775616 | a | 0 | - | | chr1 | 8775011 | 8779830 | a | 0 | - | | chr1 | 8775011 | 8778019 | a | 0 | - | | chr1 | 8775011 | 8777135 | a | 0 | - | | chr1 | 8775011 | 8776822 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 7 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmph_4t7uvn/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 8775011 8785010 - 6 chr1 8775011 8777689 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 8775011 8785010 - 6 1 chr1 8775011 8777689 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2194605 | 2203703 | a | 0 | + | | chr1 | 6552603 | 6560083 | a | 0 | - | | chr8 | 2194605 | 2203534 | a | 0 | - | | chr13 | 1046705 | 1051965 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr13 | 5160804 | 5169733 | a | 0 | - | | chr13 | 3305194 | 3310014 | a | 0 | - | | chr13 | 3924129 | 3933058 | a | 0 | - | | chr13 | 2939907 | 2948836 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 10 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpiovgt_2j/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2194605 2203703 + 1 chr1 6552603 6560083 - 1 chr13 1046705 1051965 + 1 chr13 2939907 2948836 - 1 chr13 3305194 3310014 - 1 chr13 3924129 3933058 - 1 chr13 5160804 5169733 - 1 chr17 2194605 2198765 - 1 chr22 6596876 6602897 - 1 chr8 2194605 2203534 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 2194605 2203703 + 1 1 chr1 6552603 6560083 - 1 2 chr13 1046705 1051965 + 1 3 chr13 2939907 2948836 - 1 4 chr13 3305194 3310014 - 1 5 chr13 3924129 3933058 - 1 6 chr13 5160804 5169733 - 1 7 chr17 2194605 2198765 - 1 8 chr22 6596876 6602897 - 1 9 chr8 2194605 2203534 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1122125 | 1122648 | a | 0 | + | | chr1 | 836287 | 846286 | a | 0 | + | | chr1 | 1751951 | 1759343 | a | 0 | - | | chr1 | 1 | 8797 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr3 | 3095381 | 3105381 | a | 0 | - | | chr3 | 5752876 | 5757602 | a | 0 | - | | chr11 | 60695 | 70357 | a | 0 | + | | chr17 | 5680178 | 5686597 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp9kf0gy3k/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 8797 - 1 chr1 836287 846286 + 1 chr1 1122125 1122648 + 1 chr1 1751951 1759343 - 1 chr1 3077314 3085892 - 1 chr1 6964222 6973381 - 1 chr11 60695 70357 + 1 chr17 5680178 5686597 - 1 chr3 3095381 3105381 - 1 chr3 5752876 5757602 - 1 chrX 800197 805780 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1 8797 - 1 1 chr1 836287 846286 + 1 2 chr1 1122125 1122648 + 1 3 chr1 1751951 1759343 - 1 4 chr1 3077314 3085892 - 1 5 chr1 6964222 6973381 - 1 6 chr11 60695 70357 + 1 7 chr17 5680178 5686597 - 1 8 chr3 3095381 3105381 - 1 9 chr3 5752876 5757602 - 1 10 chrX 800197 805780 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr15 | 7823149 | 7828349 | a | 0 | - | | chr15 | 4254197 | 4256177 | a | 0 | - | | chr15 | 6781453 | 6789006 | a | 0 | - | | chr15 | 3177926 | 3187590 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp32aniy7e/f1.bed) resultresultresultresultresultresultresultresultresultresult chr15 3177926 3187590 - 1 chr15 4254197 4256177 - 1 chr15 6781453 6789006 - 1 chr15 7823149 7828349 - 1 bedtools_df Chromosome Start End Strand Count 0 chr15 3177926 3187590 - 1 1 chr15 4254197 4256177 - 1 2 chr15 6781453 6789006 - 1 3 chr15 7823149 7828349 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 452154 | 452202 | a | 0 | + | | chr1 | 452154 | 459175 | a | 0 | - | | chr1 | 452154 | 458236 | a | 0 | - | | chr2 | 452154 | 455057 | a | 0 | - | | chr3 | 452154 | 455559 | a | 0 | - | | chr7 | 3402642 | 3406738 | a | 0 | - | | chr7 | 6782619 | 6782620 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 7 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpz33q_s2c/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 452154 452202 + 1 chr1 452154 459175 - 2 chr2 452154 455057 - 1 chr3 452154 455559 - 1 chr7 3402642 3406738 - 1 chr7 6782619 6782620 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 452154 452202 + 1 1 chr1 452154 459175 - 2 2 chr2 452154 455057 - 1 3 chr3 452154 455559 - 1 4 chr7 3402642 3406738 - 1 5 chr7 6782619 6782620 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8504956 | 8507007 | a | 0 | + | | chr1 | 2352521 | 2359541 | a | 0 | + | | chr16 | 6308972 | 6310336 | a | 0 | + | | chr16 | 6308972 | 6317610 | a | 0 | + | | chr16 | 9405701 | 9406396 | a | 0 | + | | chr16 | 6308972 | 6314257 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpw7uemx89/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2352521 2359541 + 1 chr1 8504956 8507007 + 1 chr16 6308972 6317610 + 3 chr16 9405701 9406396 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 2352521 2359541 + 1 1 chr1 8504956 8507007 + 1 2 chr16 6308972 6317610 + 3 3 chr16 9405701 9406396 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8091669 | 8097499 | a | 0 | - | | chr2 | 6147304 | 6150659 | a | 0 | - | | chr12 | 7372515 | 7373888 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpzvfv4g8z/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 8091669 8097499 - 1 chr12 7372515 7373888 + 1 chr2 6147304 6150659 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 8091669 8097499 - 1 1 chr12 7372515 7373888 + 1 2 chr2 6147304 6150659 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4445698 | 4448056 | a | 0 | + | | chr1 | 1855369 | 1856567 | a | 0 | + | | chr1 | 1828422 | 1828507 | a | 0 | - | | chr1 | 1855369 | 1862946 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr17 | 1855369 | 1861742 | a | 0 | + | | chr21 | 218847 | 220894 | a | 0 | + | | chrM | 5022496 | 5029335 | a | 0 | + | | chrY | 7938950 | 7939472 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 8 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp018wknv3/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1828422 1828507 - 1 chr1 1855369 1856567 + 1 chr1 1855369 1862946 - 1 chr1 4445698 4448056 + 1 chr13 2448963 2452725 - 1 chr14 1855369 1863201 + 1 chr17 1855369 1861742 + 1 chr21 218847 220894 + 1 chr8 1953842 1961419 - 1 chrM 5022496 5029335 + 1 chrY 7938950 7939472 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1828422 1828507 - 1 1 chr1 1855369 1856567 + 1 2 chr1 1855369 1862946 - 1 3 chr1 4445698 4448056 + 1 4 chr13 2448963 2452725 - 1 5 chr14 1855369 1863201 + 1 6 chr17 1855369 1861742 + 1 7 chr21 218847 220894 + 1 8 chr8 1953842 1961419 - 1 9 chrM 5022496 5029335 + 1 10 chrY 7938950 7939472 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9771936 | 9774540 | a | 0 | - | | chr6 | 4327167 | 4332422 | a | 0 | + | | chr18 | 7732090 | 7734694 | a | 0 | + | | chr21 | 3812 | 6416 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp_pj62v9e/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 9771936 9774540 - 1 chr18 7732090 7734694 + 1 chr21 3812 6416 - 1 chr6 4327167 4332422 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 9771936 9774540 - 1 1 chr18 7732090 7734694 + 1 2 chr21 3812 6416 - 1 3 chr6 4327167 4332422 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7908319 | 7916245 | a | 0 | + | | chr1 | 4696183 | 4704757 | a | 0 | + | | chr1 | 4448447 | 4454762 | a | 0 | + | | chr1 | 1 | 3451 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr15 | 1179549 | 1187478 | a | 0 | + | | chr16 | 4989428 | 4996476 | a | 0 | + | | chr17 | 1345233 | 1354736 | a | 0 | - | | chrM | 9752416 | 9760959 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 7 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp7xxq4dzt/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 3451 - 1 chr1 3338439 3346788 - 1 chr1 4448447 4454762 + 1 chr1 4696183 4704757 + 1 chr1 7908319 7916245 + 1 chr15 1179549 1187478 + 1 chr16 4989428 4996476 + 1 chr17 1345233 1354736 - 1 chr2 4905028 4912122 + 1 chr5 4004553 4004555 - 1 chrM 9752416 9760959 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1 3451 - 1 1 chr1 3338439 3346788 - 1 2 chr1 4448447 4454762 + 1 3 chr1 4696183 4704757 + 1 4 chr1 7908319 7916245 + 1 5 chr15 1179549 1187478 + 1 6 chr16 4989428 4996476 + 1 7 chr17 1345233 1354736 - 1 8 chr2 4905028 4912122 + 1 9 chr5 4004553 4004555 - 1 10 chrM 9752416 9760959 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3018768 | 3018771 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmponnzhjb0/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 3018768 3018771 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 3018768 3018771 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 238683 | 239071 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp1blkyaad/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 238683 239071 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 238683 239071 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2823579 | 2829254 | a | 0 | + | | chr1 | 2823579 | 2829254 | a | 0 | + | | chr1 | 3744748 | 3748104 | a | 0 | + | | chr1 | 6986113 | 6992787 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr14 | 7735976 | 7739390 | a | 0 | - | | chr18 | 2514058 | 2515844 | a | 0 | + | | chr22 | 6748071 | 6754153 | a | 0 | - | | chrM | 10000000 | 10007188 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 9 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp4mtzq57n/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2823579 2829254 + 2 chr1 3744748 3748104 + 1 chr1 6986113 6992787 - 1 chr14 7735976 7739390 - 1 chr18 2514058 2515844 + 1 chr2 2823579 2829254 - 1 chr22 6748071 6754153 - 1 chrM 10000000 10007188 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 2823579 2829254 + 2 1 chr1 3744748 3748104 + 1 2 chr1 6986113 6992787 - 1 3 chr14 7735976 7739390 - 1 4 chr18 2514058 2515844 + 1 5 chr2 2823579 2829254 - 1 6 chr22 6748071 6754153 - 1 7 chrM 10000000 10007188 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8842596 | 8847240 | a | 0 | + | | chr1 | 2250468 | 2256215 | a | 0 | + | | chr1 | 4831061 | 4841061 | a | 0 | - | | chr6 | 1054520 | 1061035 | a | 0 | + | | chr6 | 8359340 | 8360638 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpidl5wc5p/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2250468 2256215 + 1 chr1 4831061 4841061 - 1 chr1 8842596 8847240 + 1 chr6 1054520 1061035 + 1 chr6 8359340 8360638 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 2250468 2256215 + 1 1 chr1 4831061 4841061 - 1 2 chr1 8842596 8847240 + 1 3 chr6 1054520 1061035 + 1 4 chr6 8359340 8360638 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chrX | 8530549 | 8538628 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpdcs3p4_0/f1.bed) resultresultresultresultresultresultresultresultresultresult chrX 8530549 8538628 + 1 bedtools_df Chromosome Start End Strand Count 0 chrX 8530549 8538628 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5595264 | 5595914 | a | 0 | - | | chr1 | 3125099 | 3125101 | a | 0 | - | | chr2 | 4528790 | 4535407 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpgd1f0da7/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 3125099 3125101 - 1 chr1 5595264 5595914 - 1 chr2 4528790 4535407 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 3125099 3125101 - 1 1 chr1 5595264 5595914 - 1 2 chr2 4528790 4535407 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5494991 | 5497180 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpm21hglwj/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 5494991 5497180 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 5494991 5497180 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2861376 | 2864259 | a | 0 | + | | chr1 | 2861376 | 2868022 | a | 0 | + | | chr1 | 2861376 | 2866209 | a | 0 | + | | chr1 | 2861376 | 2863817 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr1 | 2861376 | 2869696 | a | 0 | - | | chr1 | 2861376 | 2861377 | a | 0 | - | | chr1 | 2861376 | 2868837 | a | 0 | - | | chr1 | 2861376 | 2862395 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp7kbswvh_/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2861376 2869696 - 4 chr1 2861376 2868022 + 4 chr15 2861376 2870693 - 1 chr9 2861376 2863294 - 1 chrY 2861376 2864848 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 2861376 2869696 - 4 1 chr1 2861376 2868022 + 4 2 chr15 2861376 2870693 - 1 3 chr9 2861376 2863294 - 1 4 chrY 2861376 2864848 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3709088 | 3717471 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp1u179b_6/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 3709088 3717471 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 3709088 3717471 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9257865 | 9267094 | a | 0 | + | | chr1 | 2172575 | 2176742 | a | 0 | + | | chr1 | 355246 | 361543 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpwfs3190q/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 355246 361543 + 1 chr1 2172575 2176742 + 1 chr1 9257865 9267094 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 355246 361543 + 1 1 chr1 2172575 2176742 + 1 2 chr1 9257865 9267094 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5651255 | 5660329 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpdvma718r/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 5651255 5660329 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 5651255 5660329 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr3 | 5329548 | 5332865 | a | 0 | - | | chr4 | 235049 | 242876 | a | 0 | - | | chr7 | 6666397 | 6676320 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp5wj8t652/f1.bed) resultresultresultresultresultresultresultresultresultresult chr3 5329548 5332865 - 1 chr4 235049 242876 - 1 chr7 6666397 6676320 - 1 bedtools_df Chromosome Start End Strand Count 0 chr3 5329548 5332865 - 1 1 chr4 235049 242876 - 1 2 chr7 6666397 6676320 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpwtbuujia/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1 2 + 1 __________ test_three_in_a_row[strandedness_chain416-method_chain416] __________ [gw10] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', None), method_chain = ('nearest', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:63: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('nearest', 'nearest'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:73 E (and 27 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2QAA0Y4AaeQAbIQAADgAAY=') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty 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PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty 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'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain419-method_chain419] __________ [gw6] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', None), method_chain = ('nearest', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:63: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('nearest', 'join'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:73 E (and 27 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2RAAozYKAgTzgEAAM0ABw==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ______________________________ test_merge[False] _______________________________ [gw5] linux -- Python 3.12.6 /usr/bin/python3.12 strand = False @pytest.mark.bedtools > @pytest.mark.parametrize("strand", [True, False]) tests/test_unary.py:31: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_unary.py:75: in test_merge result = gr.merge(strand=strand, count=True) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_merge( E strand=False, E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., # or any other generated value E ) sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpr9smgede/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1 2 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 10000000 | 10007956 | a | 0 | + | | chr1 | 1374899 | 1380220 | a | 0 | + | | chr1 | 2933200 | 2943099 | a | 0 | + | | chr1 | 2540706 | 2546419 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr7 | 1 | 2358 | a | 0 | - | | chr13 | 120664 | 129500 | a | 0 | + | | chr14 | 1034048 | 1042004 | a | 0 | + | | chr18 | 783117 | 787640 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpahy7ufqz/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1374899 1380220 + 1 chr1 2540706 2546419 + 1 chr1 2933200 2943099 + 1 chr1 3455834 3457774 - 1 chr1 3681536 3688794 - 1 chr1 8693487 8703486 - 1 chr1 10000000 10007956 + 1 chr13 120664 129500 + 1 chr14 1034048 1042004 + 1 chr18 783117 787640 + 1 chr7 1 2358 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1374899 1380220 1 1 chr1 2540706 2546419 1 2 chr1 2933200 2943099 1 3 chr1 3455834 3457774 1 4 chr1 3681536 3688794 1 5 chr1 8693487 8703486 1 6 chr1 10000000 10007956 1 7 chr13 120664 129500 1 8 chr14 1034048 1042004 1 9 chr18 783117 787640 1 10 chr7 1 2358 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 10000000 | 10007956 | a | 0 | + | | chr1 | 1374899 | 1380220 | a | 0 | + | | chr1 | 2933200 | 2943099 | a | 0 | + | | chr1 | 2540706 | 2546419 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr7 | 1 | 2358 | a | 0 | - | | chr13 | 3 | 8839 | a | 0 | + | | chr14 | 1034048 | 1042004 | a | 0 | + | | chr18 | 4523 | 9046 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpeosazpur/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1374899 1380220 + 1 chr1 2540706 2546419 + 1 chr1 2933200 2943099 + 1 chr1 3455834 3457774 - 1 chr1 3681536 3688794 - 1 chr1 8693487 8703486 - 1 chr1 10000000 10007956 + 1 chr13 3 8839 + 1 chr14 1034048 1042004 + 1 chr18 4523 9046 + 1 chr7 1 2358 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1374899 1380220 1 1 chr1 2540706 2546419 1 2 chr1 2933200 2943099 1 3 chr1 3455834 3457774 1 4 chr1 3681536 3688794 1 5 chr1 8693487 8703486 1 6 chr1 10000000 10007956 1 7 chr13 3 8839 1 8 chr14 1034048 1042004 1 9 chr18 4523 9046 1 10 chr7 1 2358 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3681536 | 3681793 | a | 0 | + | | chr1 | 10000000 | 10000257 | a | 0 | - | | chr1 | 1374899 | 1375156 | a | 0 | - | | chr1 | 6 | 7 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr7 | 1 | 2 | a | 0 | - | | chr13 | 5 | 6 | a | 0 | - | | chr14 | 1034048 | 1034305 | a | 0 | - | | chr18 | 4523 | 4526 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpn3vvkxca/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 6 7 - 1 chr1 1374899 1375156 - 1 chr1 2540706 2546419 - 1 chr1 2933200 2933206 - 1 chr1 3455834 3456091 - 1 chr1 3681536 3681793 + 1 chr1 10000000 10000257 - 1 chr13 5 6 - 1 chr14 1034048 1034305 - 1 chr18 4523 4526 - 1 chr7 1 2 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 6 7 1 1 chr1 1374899 1375156 1 2 chr1 2540706 2546419 1 3 chr1 2933200 2933206 1 4 chr1 3455834 3456091 1 5 chr1 3681536 3681793 1 6 chr1 10000000 10000257 1 7 chr13 5 6 1 8 chr14 1034048 1034305 1 9 chr18 4523 4526 1 10 chr7 1 2 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3681536 | 3681793 | a | 0 | + | | chr1 | 10000000 | 10000257 | a | 0 | - | | chr1 | 1374899 | 1375156 | a | 0 | - | | chr1 | 6 | 7 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr13 | 5 | 6 | a | 0 | - | | chr14 | 1034048 | 1034305 | a | 0 | - | | chr18 | 1 | 2 | a | 0 | - | | chr18 | 4523 | 4526 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpfhcubigr/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 6 7 - 1 chr1 1374899 1375156 - 1 chr1 2540706 2546419 - 1 chr1 2933200 2933206 - 1 chr1 3455834 3456091 - 1 chr1 3681536 3681793 + 1 chr1 10000000 10000257 - 1 chr13 5 6 - 1 chr14 1034048 1034305 - 1 chr18 1 2 - 1 chr18 4523 4526 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 6 7 1 1 chr1 1374899 1375156 1 2 chr1 2540706 2546419 1 3 chr1 2933200 2933206 1 4 chr1 3455834 3456091 1 5 chr1 3681536 3681793 1 6 chr1 10000000 10000257 1 7 chr13 5 6 1 8 chr14 1034048 1034305 1 9 chr18 1 2 1 10 chr18 4523 4526 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 65537 | 65546 | a | 0 | + | | chr1 | 65537 | 65546 | a | 0 | - | | chr1 | 65537 | 65794 | a | 0 | - | | chr1 | 1 | 10 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr13 | 65537 | 65546 | a | 0 | - | | chr14 | 65537 | 65546 | a | 0 | - | | chr18 | 65537 | 65546 | a | 0 | - | | chr18 | 65537 | 65546 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpv7e3aym2/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 10 - 1 chr1 65537 65794 + 6 chr13 65537 65546 - 1 chr14 65537 65546 - 1 chr18 65537 65546 - 2 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1 10 1 1 chr1 65537 65794 6 2 chr13 65537 65546 1 3 chr14 65537 65546 1 4 chr18 65537 65546 2 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 65537 | 65794 | a | 0 | + | | chr1 | 65537 | 65794 | a | 0 | - | | chr1 | 65537 | 65794 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr13 | 65537 | 65794 | a | 0 | - | | chr14 | 65537 | 65794 | a | 0 | - | | chr18 | 65537 | 65794 | a | 0 | - | | chr18 | 65537 | 65794 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpai0b3q3t/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2 - 1 chr1 65537 65794 + 6 chr13 65537 65794 - 1 chr14 65537 65794 - 1 chr18 65537 65794 - 2 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1 2 1 1 chr1 65537 65794 6 2 chr13 65537 65794 1 3 chr14 65537 65794 1 4 chr18 65537 65794 2 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 65537 | 65794 | a | 0 | + | | chr1 | 65537 | 65794 | a | 0 | - | | chr1 | 65537 | 65794 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr13 | 65537 | 65794 | a | 0 | - | | chr18 | 65537 | 65794 | a | 0 | - | | chr18 | 65537 | 65794 | a | 0 | - | | chr18 | 65537 | 65794 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpeppbqbna/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2 - 1 chr1 65537 65794 + 6 chr13 65537 65794 - 1 chr18 65537 65794 - 3 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1 2 1 1 chr1 65537 65794 6 2 chr13 65537 65794 1 3 chr18 65537 65794 3 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1356206 | 1360323 | a | 0 | - | | chr8 | 9890714 | 9896059 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpe4sz1wi_/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1356206 1360323 - 1 chr8 9890714 9896059 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1356206 1360323 1 1 chr8 9890714 9896059 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1356206 | 1360323 | a | 0 | - | | chr8 | 9890714 | 9896059 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpscovwgmx/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1356206 1360323 - 1 chr8 9890714 9896059 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1356206 1360323 1 1 chr8 9890714 9896059 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmprrwrrd_0/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1 2 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpjgw88zns/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1 2 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp6nmffg6k/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1 2 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpvzpo9js4/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1 2 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp2o5lklzm/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1 2 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5351342 | 5359315 | a | 0 | + | | chr1 | 5351342 | 5360880 | a | 0 | + | | chr1 | 5351342 | 5352240 | a | 0 | - | | chr1 | 5351342 | 5355064 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr1 | 5351342 | 5352240 | a | 0 | - | | chr1 | 5351342 | 5355064 | a | 0 | - | | chr1 | 242768 | 246170 | a | 0 | - | | chr1 | 5351342 | 5351917 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 9 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpe7xy9ur8/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 242768 246170 - 1 chr1 5351342 5360880 - 5 chr4 5351342 5359106 - 2 chr8 5189045 5198481 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 242768 246170 1 1 chr1 5351342 5360880 5 2 chr4 5351342 5359106 2 3 chr8 5189045 5198481 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8509605 | 8514979 | a | 0 | - | | chr1 | 5812882 | 5817658 | a | 0 | - | | chr5 | 9731623 | 9738198 | a | 0 | - | | chr13 | 3072006 | 3078906 | a | 0 | - | | chr15 | 6517970 | 6522031 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpm_avqrz1/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 5812882 5817658 - 1 chr1 8509605 8514979 - 1 chr13 3072006 3078906 - 1 chr15 6517970 6522031 - 1 chr5 9731623 9738198 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 5812882 5817658 1 1 chr1 8509605 8514979 1 2 chr13 3072006 3078906 1 3 chr15 6517970 6522031 1 4 chr5 9731623 9738198 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9527290 | 9531639 | a | 0 | - | | chr1 | 327488 | 336296 | a | 0 | - | | chr4 | 6932430 | 6941541 | a | 0 | - | | chr11 | 16376 | 16644 | a | 0 | - | | chr12 | 8936924 | 8942094 | a | 0 | + | | chr18 | 6990627 | 6991255 | a | 0 | + | | chrX | 9976354 | 9982002 | a | 0 | + | | chrX | 9937788 | 9943222 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 8 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpe8h3i979/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 327488 336296 - 1 chr1 9527290 9531639 - 1 chr11 16376 16644 - 1 chr12 8936924 8942094 + 1 chr18 6990627 6991255 + 1 chr4 6932430 6941541 - 1 chrX 9937788 9943222 - 1 chrX 9976354 9982002 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 327488 336296 1 1 chr1 9527290 9531639 1 2 chr11 16376 16644 1 3 chr12 8936924 8942094 1 4 chr18 6990627 6991255 1 5 chr4 6932430 6941541 1 6 chrX 9937788 9943222 1 7 chrX 9976354 9982002 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1159417 | 1167687 | a | 0 | + | | chr1 | 8682423 | 8691673 | a | 0 | + | | chr1 | 6006769 | 6015516 | a | 0 | + | | chr1 | 215777 | 217667 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmprq911mlg/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 215777 217667 - 1 chr1 1159417 1167687 + 1 chr1 6006769 6015516 + 1 chr1 8682423 8691673 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 215777 217667 1 1 chr1 1159417 1167687 1 2 chr1 6006769 6015516 1 3 chr1 8682423 8691673 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7254424 | 7262450 | a | 0 | + | | chr1 | 7254424 | 7256773 | a | 0 | + | | chr1 | 7254424 | 7256049 | a | 0 | + | | chr1 | 7254424 | 7257174 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr1 | 7254424 | 7262323 | a | 0 | - | | chr1 | 7254424 | 7260271 | a | 0 | - | | chr1 | 7254424 | 7262211 | a | 0 | - | | chr1 | 7254424 | 7261651 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmppl63m_0s/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 7254424 7262450 + 9 chr10 7254424 7256811 + 1 chrX 7254424 7254491 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 7254424 7262450 9 1 chr10 7254424 7256811 1 2 chrX 7254424 7254491 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3732086 | 3732565 | a | 0 | - | | chr15 | 8071953 | 8074063 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpm_qh9aw9/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 3732086 3732565 - 1 chr15 8071953 8074063 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 3732086 3732565 1 1 chr15 8071953 8074063 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9465527 | 9475524 | a | 0 | + | | chr1 | 7143198 | 7148145 | a | 0 | + | | chr1 | 28570 | 37566 | a | 0 | - | | chr1 | 9437231 | 9441714 | a | 0 | - | | chr1 | 3488287 | 3497773 | a | 0 | - | | chr22 | 7745138 | 7746322 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpvnx0960w/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 28570 37566 - 1 chr1 3488287 3497773 - 1 chr1 7143198 7148145 + 1 chr1 9437231 9441714 - 1 chr1 9465527 9475524 + 1 chr22 7745138 7746322 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 28570 37566 1 1 chr1 3488287 3497773 1 2 chr1 7143198 7148145 1 3 chr1 9437231 9441714 1 4 chr1 9465527 9475524 1 5 chr22 7745138 7746322 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9985551 | 9989182 | a | 0 | + | | chr1 | 8200326 | 8203946 | a | 0 | - | | chrM | 8459899 | 8468037 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp5oq9ka4w/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 8200326 8203946 - 1 chr1 9985551 9989182 + 1 chrM 8459899 8468037 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 8200326 8203946 1 1 chr1 9985551 9989182 1 2 chrM 8459899 8468037 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3541298 | 3550742 | a | 0 | + | | chr1 | 1747333 | 1756526 | a | 0 | + | | chr1 | 7491062 | 7500506 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpda5trd2e/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1747333 1756526 + 1 chr1 3541298 3550742 + 1 chr1 7491062 7500506 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1747333 1756526 1 1 chr1 3541298 3550742 1 2 chr1 7491062 7500506 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4118470 | 4124682 | a | 0 | + | | chr1 | 1984836 | 1987754 | a | 0 | + | | chr1 | 7196734 | 7204621 | a | 0 | - | | chr1 | 2850902 | 2858892 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr1 | 22139 | 28351 | a | 0 | - | | chr1 | 1515897 | 1517048 | a | 0 | - | | chr1 | 8039445 | 8045657 | a | 0 | - | | chr1 | 2189365 | 2194583 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp1wfmbpl5/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 22139 28351 - 1 chr1 1382477 1389202 - 1 chr1 1515897 1517048 - 1 chr1 1984836 1987754 + 1 chr1 2189365 2194583 - 1 chr1 2850902 2858892 - 1 chr1 4118470 4124682 + 1 chr1 4917216 4917296 - 1 chr1 5079818 5086030 - 1 chr1 7196734 7204621 - 1 chr1 8039445 8045657 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 22139 28351 1 1 chr1 1382477 1389202 1 2 chr1 1515897 1517048 1 3 chr1 1984836 1987754 1 4 chr1 2189365 2194583 1 5 chr1 2850902 2858892 1 6 chr1 4118470 4124682 1 7 chr1 4917216 4917296 1 8 chr1 5079818 5086030 1 9 chr1 7196734 7204621 1 10 chr1 8039445 8045657 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 204715 | 213294 | a | 0 | - | | chr21 | 2388738 | 2388739 | a | 0 | - | | chr21 | 1389364 | 1397943 | a | 0 | - | | chrX | 1301812 | 1303988 | a | 0 | + | | chrY | 2908993 | 2917572 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp0qmexn7g/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 204715 213294 - 1 chr21 1389364 1397943 - 1 chr21 2388738 2388739 - 1 chrX 1301812 1303988 + 1 chrY 2908993 2917572 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 204715 213294 1 1 chr21 1389364 1397943 1 2 chr21 2388738 2388739 1 3 chrX 1301812 1303988 1 4 chrY 2908993 2917572 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2892834 | 2895459 | a | 0 | + | | chr1 | 7580431 | 7583041 | a | 0 | - | | chr2 | 3736670 | 3746186 | a | 0 | - | | chr6 | 10000000 | 10006152 | a | 0 | + | | chr13 | 728441 | 732991 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp00blt_nd/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2892834 2895459 + 1 chr1 7580431 7583041 - 1 chr13 728441 732991 + 1 chr2 3736670 3746186 - 1 chr6 10000000 10006152 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 2892834 2895459 1 1 chr1 7580431 7583041 1 2 chr13 728441 732991 1 3 chr2 3736670 3746186 1 4 chr6 10000000 10006152 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 733512 | 736104 | a | 0 | - | | chr1 | 2333921 | 2343087 | a | 0 | - | | chr14 | 2441938 | 2443947 | a | 0 | + | | chr14 | 4594533 | 4603290 | a | 0 | - | | chrM | 7503148 | 7508607 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpzsz666g4/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 733512 736104 - 1 chr1 2333921 2343087 - 1 chr14 2441938 2443947 + 1 chr14 4594533 4603290 - 1 chrM 7503148 7508607 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 733512 736104 1 1 chr1 2333921 2343087 1 2 chr14 2441938 2443947 1 3 chr14 4594533 4603290 1 4 chrM 7503148 7508607 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 383634 | 385369 | a | 0 | + | | chr22 | 1 | 288 | a | 0 | + | | chr22 | 6899924 | 6901744 | a | 0 | + | | chr22 | 6085586 | 6085841 | a | 0 | - | | chr22 | 3865920 | 3869533 | a | 0 | - | | chr22 | 9320762 | 9327251 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpt1weyar_/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 383634 385369 + 1 chr22 1 288 + 1 chr22 3865920 3869533 - 1 chr22 6085586 6085841 - 1 chr22 6899924 6901744 + 1 chr22 9320762 9327251 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 383634 385369 1 1 chr22 1 288 1 2 chr22 3865920 3869533 1 3 chr22 6085586 6085841 1 4 chr22 6899924 6901744 1 5 chr22 9320762 9327251 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4721867 | 4726007 | a | 0 | + | | chr1 | 460529 | 464669 | a | 0 | + | | chr1 | 8191628 | 8192495 | a | 0 | + | | chr2 | 9615302 | 9623321 | a | 0 | + | | chr22 | 7269950 | 7272845 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp8id4ls1t/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 460529 464669 + 1 chr1 4721867 4726007 + 1 chr1 8191628 8192495 + 1 chr2 9615302 9623321 + 1 chr22 7269950 7272845 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 460529 464669 1 1 chr1 4721867 4726007 1 2 chr1 8191628 8192495 1 3 chr2 9615302 9623321 1 4 chr22 7269950 7272845 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7735048 | 7741306 | a | 0 | - | | chr9 | 5148256 | 5156809 | a | 0 | + | | chr9 | 9020865 | 9026430 | a | 0 | - | | chr10 | 6943860 | 6945686 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr10 | 6943860 | 6945686 | a | 0 | + | | chr10 | 2745314 | 2749247 | a | 0 | + | | chr10 | 8477767 | 8483332 | a | 0 | + | | chr10 | 4761098 | 4763069 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 10 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpv6iyy0g2/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 7735048 7741306 - 1 chr10 2745314 2749247 + 1 chr10 4761098 4763069 - 1 chr10 6943860 6945686 + 1 chr10 8477767 8483332 + 1 chr16 6553199 6556555 - 1 chr21 6007532 6017532 - 1 chr22 2878540 2885602 - 1 chr9 5148256 5156809 + 1 chr9 9020865 9026430 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 7735048 7741306 1 1 chr10 2745314 2749247 1 2 chr10 4761098 4763069 1 3 chr10 6943860 6945686 1 4 chr10 8477767 8483332 1 5 chr16 6553199 6556555 1 6 chr21 6007532 6017532 1 7 chr22 2878540 2885602 1 8 chr9 5148256 5156809 1 9 chr9 9020865 9026430 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr9 | 4729626 | 4738141 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpprxp__kr/f1.bed) resultresultresultresultresultresultresultresultresultresult chr9 4729626 4738141 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr9 4729626 4738141 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1375236 | 1381305 | a | 0 | + | | chr13 | 8746672 | 8755158 | a | 0 | - | | chr14 | 6539996 | 6548313 | a | 0 | - | | chr19 | 723644 | 729396 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp1_sw69ed/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1375236 1381305 + 1 chr13 8746672 8755158 - 1 chr14 6539996 6548313 - 1 chr19 723644 729396 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1375236 1381305 1 1 chr13 8746672 8755158 1 2 chr14 6539996 6548313 1 3 chr19 723644 729396 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr13 | 8580900 | 8586878 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp9t5m2rem/f1.bed) resultresultresultresultresultresultresultresultresultresult chr13 8580900 8586878 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr13 8580900 8586878 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4959951 | 4968719 | a | 0 | + | | chr9 | 1 | 7406 | a | 0 | - | | chr14 | 4959951 | 4961246 | a | 0 | + | | chrX | 4959951 | 4963277 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmprgd_cg6i/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 4959951 4968719 + 1 chr14 4959951 4961246 + 1 chr9 1 7406 - 1 chrX 4959951 4963277 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 4959951 4968719 1 1 chr14 4959951 4961246 1 2 chr9 1 7406 1 3 chrX 4959951 4963277 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7347025 | 7349750 | a | 0 | + | | chr1 | 8097145 | 8102491 | a | 0 | + | | chr1 | 9639658 | 9646735 | a | 0 | + | | chr1 | 8539703 | 8548251 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr2 | 2789743 | 2790970 | a | 0 | + | | chr2 | 5356076 | 5362917 | a | 0 | - | | chr3 | 7361989 | 7369000 | a | 0 | + | | chr17 | 4942976 | 4946387 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp_hiuqhzd/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 7347025 7349750 + 1 chr1 8097145 8102491 + 1 chr1 8110159 8115045 - 1 chr1 8539703 8548251 + 1 chr1 9639658 9646735 + 1 chr1 9941413 9944446 - 1 chr1 9999999 10008849 - 1 chr17 4942976 4946387 - 1 chr2 2789743 2790970 + 1 chr2 5356076 5362917 - 1 chr3 7361989 7369000 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 7347025 7349750 1 1 chr1 8097145 8102491 1 2 chr1 8110159 8115045 1 3 chr1 8539703 8548251 1 4 chr1 9639658 9646735 1 5 chr1 9941413 9944446 1 6 chr1 9999999 10008849 1 7 chr17 4942976 4946387 1 8 chr2 2789743 2790970 1 9 chr2 5356076 5362917 1 10 chr3 7361989 7369000 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2469822 | 2469823 | a | 0 | + | | chr1 | 1429688 | 1439463 | a | 0 | + | | chr1 | 7882181 | 7886421 | a | 0 | + | | chr1 | 1613711 | 1616670 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr12 | 4155330 | 4161820 | a | 0 | - | | chr14 | 1510786 | 1515137 | a | 0 | - | | chr16 | 7696604 | 7704256 | a | 0 | + | | chr16 | 5802736 | 5807079 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp8slblhc2/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1429688 1439463 + 1 chr1 1613711 1616670 - 1 chr1 2469822 2469823 + 1 chr1 5929162 5932823 - 1 chr1 7882181 7886421 + 1 chr1 10000000 10006414 - 1 chr12 4155330 4161820 - 1 chr14 1510786 1515137 - 1 chr16 5802736 5807079 - 1 chr16 7696604 7704256 + 1 chr4 2689816 2692873 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1429688 1439463 1 1 chr1 1613711 1616670 1 2 chr1 2469822 2469823 1 3 chr1 5929162 5932823 1 4 chr1 7882181 7886421 1 5 chr1 10000000 10006414 1 6 chr12 4155330 4161820 1 7 chr14 1510786 1515137 1 8 chr16 5802736 5807079 1 9 chr16 7696604 7704256 1 10 chr4 2689816 2692873 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 399615 | 400588 | a | 0 | + | | chr1 | 6059426 | 6066060 | a | 0 | + | | chr1 | 7974231 | 7983696 | a | 0 | + | | chr1 | 3394230 | 3402579 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr15 | 8910629 | 8913117 | a | 0 | + | | chr19 | 5067489 | 5073810 | a | 0 | + | | chr19 | 4546682 | 4554858 | a | 0 | + | | chr22 | 4546682 | 4549792 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmph16p_73p/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 399615 400588 + 1 chr1 1217212 1220057 - 1 chr1 3394230 3402579 + 1 chr1 4103161 4113027 - 1 chr1 4546682 4548887 - 1 chr1 6059426 6066060 + 1 chr1 7974231 7983696 + 1 chr15 8910629 8913117 + 1 chr19 4546682 4554858 + 1 chr19 5067489 5073810 + 1 chr22 4546682 4549792 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 399615 400588 1 1 chr1 1217212 1220057 1 2 chr1 3394230 3402579 1 3 chr1 4103161 4113027 1 4 chr1 4546682 4548887 1 5 chr1 6059426 6066060 1 6 chr1 7974231 7983696 1 7 chr15 8910629 8913117 1 8 chr19 4546682 4554858 1 9 chr19 5067489 5073810 1 10 chr22 4546682 4549792 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7261771 | 7262485 | a | 0 | + | | chr3 | 7606591 | 7608715 | a | 0 | + | | chr7 | 7261771 | 7261909 | a | 0 | + | | chr16 | 7261771 | 7271770 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chrY | 7261771 | 7263258 | a | 0 | + | | chrY | 6752546 | 6754670 | a | 0 | - | | chrY | 6252521 | 6261527 | a | 0 | - | | chrY | 7261771 | 7268838 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp_m7dre95/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 7261771 7262485 + 1 chr16 7261771 7271770 - 1 chr21 5616153 5618277 - 1 chr3 7606591 7608715 + 1 chr7 7261771 7261909 + 1 chrY 6252521 6261527 - 1 chrY 6752546 6754670 - 1 chrY 7261771 7270073 + 4 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 7261771 7262485 1 1 chr16 7261771 7271770 1 2 chr21 5616153 5618277 1 3 chr3 7606591 7608715 1 4 chr7 7261771 7261909 1 5 chrY 6252521 6261527 1 6 chrY 6752546 6754670 1 7 chrY 7261771 7270073 4 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 574882 | 580486 | a | 0 | + | | chr1 | 3484313 | 3494312 | a | 0 | + | | chr1 | 333019 | 343018 | a | 0 | - | | chr1 | 3878636 | 3879352 | a | 0 | - | | chr1 | 8572593 | 8573067 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpmv052k6p/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 333019 343018 - 1 chr1 574882 580486 + 1 chr1 3484313 3494312 + 1 chr1 3878636 3879352 - 1 chr1 8572593 8573067 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 333019 343018 1 1 chr1 574882 580486 1 2 chr1 3484313 3494312 1 3 chr1 3878636 3879352 1 4 chr1 8572593 8573067 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr5 | 5191717 | 5195062 | a | 0 | + | | chr8 | 2 | 7919 | a | 0 | + | | chr21 | 8980824 | 8986991 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp9tslsl1o/f1.bed) resultresultresultresultresultresultresultresultresultresult chr21 8980824 8986991 - 1 chr5 5191717 5195062 + 1 chr8 2 7919 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr21 8980824 8986991 1 1 chr5 5191717 5195062 1 2 chr8 2 7919 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 471128 | 480885 | a | 0 | + | | chr1 | 1800945 | 1806117 | a | 0 | - | | chr11 | 9195512 | 9202154 | a | 0 | + | | chr13 | 10000000 | 10005690 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr13 | 10000000 | 10004727 | a | 0 | + | | chr13 | 4018542 | 4020286 | a | 0 | + | | chr13 | 2089957 | 2096480 | a | 0 | - | | chr13 | 9195512 | 9201598 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpsr9g4aww/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 471128 480885 + 1 chr1 1800945 1806117 - 1 chr11 9195512 9202154 + 1 chr13 2089957 2096480 - 1 chr13 4018542 4020286 + 1 chr13 9195512 9204624 - 2 chr13 10000000 10005690 + 2 chrX 1564565 1571197 + 1 chrY 6394363 6398020 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 471128 480885 1 1 chr1 1800945 1806117 1 2 chr11 9195512 9202154 1 3 chr13 2089957 2096480 1 4 chr13 4018542 4020286 1 5 chr13 9195512 9204624 2 6 chr13 10000000 10005690 2 7 chrX 1564565 1571197 1 8 chrY 6394363 6398020 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr20 | 2978286 | 2988285 | a | 0 | - | | chr22 | 7625850 | 7627178 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpmufdbspj/f1.bed) resultresultresultresultresultresultresultresultresultresult chr20 2978286 2988285 - 1 chr22 7625850 7627178 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr20 2978286 2988285 1 1 chr22 7625850 7627178 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4338412 | 4340620 | a | 0 | - | | chrM | 8396537 | 8400882 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpugn75sy1/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 4338412 4340620 - 1 chrM 8396537 8400882 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 4338412 4340620 1 1 chrM 8396537 8400882 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2507838 | 2516392 | a | 0 | + | | chr1 | 811210 | 813044 | a | 0 | + | | chr1 | 2702603 | 2708752 | a | 0 | + | | chr1 | 9980505 | 9980507 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr1 | 7494173 | 7495940 | a | 0 | - | | chr1 | 7753684 | 7756081 | a | 0 | - | | chr1 | 4973368 | 4974474 | a | 0 | - | | chr1 | 5246916 | 5252887 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpj596jksc/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 811210 813044 + 1 chr1 2507838 2516392 + 1 chr1 2702603 2708752 + 1 chr1 4973368 4974474 - 1 chr1 5246916 5252887 - 1 chr1 7047148 7055798 + 1 chr1 7494173 7495940 - 1 chr1 7753684 7756081 - 1 chr1 9980505 9980507 + 1 chr14 5246916 5256916 + 1 chrM 6291136 6294235 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 811210 813044 1 1 chr1 2507838 2516392 1 2 chr1 2702603 2708752 1 3 chr1 4973368 4974474 1 4 chr1 5246916 5252887 1 5 chr1 7047148 7055798 1 6 chr1 7494173 7495940 1 7 chr1 7753684 7756081 1 8 chr1 9980505 9980507 1 9 chr14 5246916 5256916 1 10 chrM 6291136 6294235 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 459403 | 462114 | a | 0 | + | | chr1 | 7960960 | 7964539 | a | 0 | + | | chr1 | 1581371 | 1583935 | a | 0 | + | | chr1 | 4965032 | 4966042 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr1 | 3542888 | 3550645 | a | 0 | - | | chr1 | 2416118 | 2422699 | a | 0 | - | | chr1 | 7338642 | 7347931 | a | 0 | - | | chr1 | 4578638 | 4580112 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpvf1vnbvj/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 459403 462114 + 1 chr1 1581371 1583935 + 1 chr1 2342390 2350652 - 1 chr1 2416118 2422699 - 1 chr1 3542888 3550645 - 1 chr1 4578638 4580112 - 1 chr1 4695133 4696845 - 1 chr1 4965032 4966042 + 1 chr1 7338642 7347931 - 1 chr1 7960960 7964539 + 1 chrY 2845058 2846872 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 459403 462114 1 1 chr1 1581371 1583935 1 2 chr1 2342390 2350652 1 3 chr1 2416118 2422699 1 4 chr1 3542888 3550645 1 5 chr1 4578638 4580112 1 6 chr1 4695133 4696845 1 7 chr1 4965032 4966042 1 8 chr1 7338642 7347931 1 9 chr1 7960960 7964539 1 10 chrY 2845058 2846872 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 586378 | 587048 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpacs5ge9s/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 586378 587048 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 586378 587048 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7437994 | 7441957 | a | 0 | - | | chr1 | 8224127 | 8233046 | a | 0 | - | | chr1 | 6099600 | 6108205 | a | 0 | - | | chr1 | 4806135 | 4809206 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr9 | 1 | 8283 | a | 0 | - | | chr9 | 3321767 | 3324788 | a | 0 | - | | chr13 | 6463921 | 6471101 | a | 0 | - | | chrX | 5278590 | 5287108 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpfn3tly9k/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 4408267 4416319 - 1 chr1 4806135 4809206 - 1 chr1 6099600 6108205 - 1 chr1 7437994 7441957 - 1 chr1 8224127 8233046 - 1 chr13 6463921 6471101 - 1 chr5 388097 393637 - 1 chr6 4476657 4478363 - 1 chr9 1 8283 - 1 chr9 3321767 3324788 - 1 chrX 5278590 5287108 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 4408267 4416319 1 1 chr1 4806135 4809206 1 2 chr1 6099600 6108205 1 3 chr1 7437994 7441957 1 4 chr1 8224127 8233046 1 5 chr13 6463921 6471101 1 6 chr5 388097 393637 1 7 chr6 4476657 4478363 1 8 chr9 1 8283 1 9 chr9 3321767 3324788 1 10 chrX 5278590 5287108 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr3 | 9816171 | 9822754 | a | 0 | - | | chr22 | 7558306 | 7564889 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpgs32xofl/f1.bed) resultresultresultresultresultresultresultresultresultresult chr22 7558306 7564889 + 1 chr3 9816171 9822754 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr22 7558306 7564889 1 1 chr3 9816171 9822754 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6043775 | 6048628 | a | 0 | + | | chr1 | 2210115 | 2216158 | a | 0 | + | | chr1 | 9999999 | 10005902 | a | 0 | + | | chr1 | 9999999 | 10009002 | a | 0 | + | | chr1 | 1714241 | 1720047 | a | 0 | + | | chr1 | 5577522 | 5585985 | a | 0 | - | | chr18 | 1062392 | 1068698 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 7 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp1h7jcy9b/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1714241 1720047 + 1 chr1 2210115 2216158 + 1 chr1 5577522 5585985 - 1 chr1 6043775 6048628 + 1 chr1 9999999 10009002 + 2 chr18 1062392 1068698 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1714241 1720047 1 1 chr1 2210115 2216158 1 2 chr1 5577522 5585985 1 3 chr1 6043775 6048628 1 4 chr1 9999999 10009002 2 5 chr18 1062392 1068698 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8270979 | 8277969 | a | 0 | + | | chr1 | 6207022 | 6213495 | a | 0 | + | | chr1 | 9397423 | 9405206 | a | 0 | + | | chr5 | 7788300 | 7790698 | a | 0 | + | | chr13 | 9286813 | 9287357 | a | 0 | + | | chr16 | 999471 | 1008119 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpr4ibojcj/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 6207022 6213495 + 1 chr1 8270979 8277969 + 1 chr1 9397423 9405206 + 1 chr13 9286813 9287357 + 1 chr16 999471 1008119 + 1 chr5 7788300 7790698 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 6207022 6213495 1 1 chr1 8270979 8277969 1 2 chr1 9397423 9405206 1 3 chr13 9286813 9287357 1 4 chr16 999471 1008119 1 5 chr5 7788300 7790698 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7553453 | 7560537 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpmgxh6o3i/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 7553453 7560537 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 7553453 7560537 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1246968 | 1251151 | a | 0 | + | | chr1 | 6031022 | 6039509 | a | 0 | + | | chr1 | 5684706 | 5689088 | a | 0 | + | | chr5 | 5196317 | 5198879 | a | 0 | - | | chrX | 6892459 | 6894027 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmps3fbtgyw/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1246968 1251151 + 1 chr1 5684706 5689088 + 1 chr1 6031022 6039509 + 1 chr5 5196317 5198879 - 1 chrX 6892459 6894027 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1246968 1251151 1 1 chr1 5684706 5689088 1 2 chr1 6031022 6039509 1 3 chr5 5196317 5198879 1 4 chrX 6892459 6894027 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9275360 | 9282104 | a | 0 | + | | chr9 | 4833481 | 4840225 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpybn_x1as/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 9275360 9282104 + 1 chr9 4833481 4840225 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 9275360 9282104 1 1 chr9 4833481 4840225 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2423601 | 2427783 | a | 0 | + | | chr1 | 8953926 | 8960591 | a | 0 | + | | chr1 | 8804889 | 8805793 | a | 0 | + | | chr1 | 10000000 | 10006031 | a | 0 | - | | chr1 | 5338125 | 5342332 | a | 0 | - | | chr1 | 4172282 | 4174370 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp6c0oi3ea/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2423601 2427783 + 1 chr1 4172282 4174370 - 1 chr1 5338125 5342332 - 1 chr1 8804889 8805793 + 1 chr1 8953926 8960591 + 1 chr1 10000000 10006031 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 2423601 2427783 1 1 chr1 4172282 4174370 1 2 chr1 5338125 5342332 1 3 chr1 8804889 8805793 1 4 chr1 8953926 8960591 1 5 chr1 10000000 10006031 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7024755 | 7024756 | a | 0 | + | | chr1 | 7685342 | 7693744 | a | 0 | + | | chr1 | 7510237 | 7514912 | a | 0 | + | | chr1 | 6612202 | 6616316 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr15 | 2181167 | 2190694 | a | 0 | + | | chr15 | 913515 | 919384 | a | 0 | + | | chr15 | 96222 | 105486 | a | 0 | - | | chr17 | 8664627 | 8669543 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpcw3hk0xc/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1989749 1998630 - 1 chr1 4370904 4380454 - 1 chr1 6612202 6616316 - 1 chr1 7024755 7024756 + 1 chr1 7510237 7514912 + 1 chr1 7685342 7693744 + 1 chr15 96222 105486 - 1 chr15 913515 919384 + 1 chr15 2181167 2190694 + 1 chr17 8664627 8669543 + 1 chrX 1754972 1760557 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1989749 1998630 1 1 chr1 4370904 4380454 1 2 chr1 6612202 6616316 1 3 chr1 7024755 7024756 1 4 chr1 7510237 7514912 1 5 chr1 7685342 7693744 1 6 chr15 96222 105486 1 7 chr15 913515 919384 1 8 chr15 2181167 2190694 1 9 chr17 8664627 8669543 1 10 chrX 1754972 1760557 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 679390 | 680494 | a | 0 | + | | chr1 | 2464071 | 2467226 | a | 0 | + | | chr1 | 9999999 | 10004368 | a | 0 | - | | chr2 | 3939848 | 3946341 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr14 | 2867202 | 2873691 | a | 0 | + | | chr14 | 1 | 2 | a | 0 | - | | chr14 | 373945 | 378134 | a | 0 | - | | chr20 | 12413 | 22364 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 7 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpw7lbsa7l/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 679390 680494 + 1 chr1 2464071 2467226 + 1 chr1 9999999 10004368 - 1 chr10 5586580 5587972 - 1 chr14 1 2 - 1 chr14 373945 378134 - 1 chr14 2867202 2873691 + 1 chr2 3939848 3946341 + 1 chr20 12413 22364 + 1 chr21 1350793 1358903 + 1 chrX 5794764 5799060 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 679390 680494 1 1 chr1 2464071 2467226 1 2 chr1 9999999 10004368 1 3 chr10 5586580 5587972 1 4 chr14 1 2 1 5 chr14 373945 378134 1 6 chr14 2867202 2873691 1 7 chr2 3939848 3946341 1 8 chr20 12413 22364 1 9 chr21 1350793 1358903 1 10 chrX 5794764 5799060 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8637839 | 8643645 | a | 0 | + | | chr1 | 8419720 | 8423647 | a | 0 | + | | chrX | 8493887 | 8496099 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmppxw8337j/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 8419720 8423647 + 1 chr1 8637839 8643645 + 1 chrX 8493887 8496099 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 8419720 8423647 1 1 chr1 8637839 8643645 1 2 chrX 8493887 8496099 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9504518 | 9510780 | a | 0 | - | | chr13 | 2651224 | 2652026 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpn5ihetck/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 9504518 9510780 - 1 chr13 2651224 2652026 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 9504518 9510780 1 1 chr13 2651224 2652026 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9987970 | 9989194 | a | 0 | + | | chr1 | 9987970 | 9990081 | a | 0 | + | | chr1 | 3063584 | 3069815 | a | 0 | + | | chr1 | 4929826 | 4936574 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr6 | 9987970 | 9994739 | a | 0 | - | | chr10 | 9987970 | 9993694 | a | 0 | - | | chr13 | 808268 | 817558 | a | 0 | + | | chr17 | 3700221 | 3701756 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 7 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpgmyqydzs/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 3063584 3069815 + 1 chr1 4929826 4936574 - 1 chr1 9675293 9677367 - 1 chr1 9987970 9990081 + 2 chr10 9987970 9993694 - 1 chr13 808268 817558 + 1 chr17 3700221 3701756 - 1 chr2 9987970 9996687 + 1 chr3 4782155 4782935 + 1 chr6 9987970 9994739 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 3063584 3069815 1 1 chr1 4929826 4936574 1 2 chr1 9675293 9677367 1 3 chr1 9987970 9990081 2 4 chr10 9987970 9993694 1 5 chr13 808268 817558 1 6 chr17 3700221 3701756 1 7 chr2 9987970 9996687 1 8 chr3 4782155 4782935 1 9 chr6 9987970 9994739 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4780357 | 4789914 | a | 0 | + | | chr1 | 5880780 | 5883151 | a | 0 | - | | chr1 | 2212748 | 2221829 | a | 0 | - | | chr5 | 4393753 | 4402837 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr21 | 4613958 | 4617626 | a | 0 | + | | chr21 | 2905538 | 2913070 | a | 0 | - | | chr21 | 553248 | 556531 | a | 0 | - | | chr21 | 2973413 | 2974906 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 10 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpz5qeqd8i/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2212748 2221829 - 1 chr1 4780357 4789914 + 1 chr1 5880780 5883151 - 1 chr12 4286149 4287572 - 1 chr21 553248 556531 - 1 chr21 2905538 2913070 - 1 chr21 2973413 2974906 - 1 chr21 4263279 4270656 + 1 chr21 4613958 4617626 + 1 chr5 4393753 4402837 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 2212748 2221829 1 1 chr1 4780357 4789914 1 2 chr1 5880780 5883151 1 3 chr12 4286149 4287572 1 4 chr21 553248 556531 1 5 chr21 2905538 2913070 1 6 chr21 2973413 2974906 1 7 chr21 4263279 4270656 1 8 chr21 4613958 4617626 1 9 chr5 4393753 4402837 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3355401 | 3357554 | a | 0 | + | | chr1 | 9607816 | 9615136 | a | 0 | + | | chr1 | 3429083 | 3438686 | a | 0 | - | | chr12 | 2289850 | 2296047 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp4lyrnfvj/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 3355401 3357554 + 1 chr1 3429083 3438686 - 1 chr1 9607816 9615136 + 1 chr12 2289850 2296047 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 3355401 3357554 1 1 chr1 3429083 3438686 1 2 chr1 9607816 9615136 1 3 chr12 2289850 2296047 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 462498 | 471749 | a | 0 | + | | chr1 | 491664 | 501663 | a | 0 | - | | chr1 | 7952718 | 7961984 | a | 0 | - | | chr12 | 8012536 | 8016491 | a | 0 | + | | chr22 | 2989801 | 2991758 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpzc7fnwjm/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 462498 471749 + 1 chr1 491664 501663 - 1 chr1 7952718 7961984 - 1 chr12 8012536 8016491 + 1 chr22 2989801 2991758 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 462498 471749 1 1 chr1 491664 501663 1 2 chr1 7952718 7961984 1 3 chr12 8012536 8016491 1 4 chr22 2989801 2991758 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1304758 | 1313436 | a | 0 | + | | chr1 | 4030315 | 4039498 | a | 0 | - | | chr1 | 9150208 | 9155029 | a | 0 | - | | chr1 | 1757834 | 1760660 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr16 | 2 | 4365 | a | 0 | - | | chr18 | 618317 | 624649 | a | 0 | - | | chr20 | 9654994 | 9655992 | a | 0 | - | | chrY | 613201 | 621729 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 8 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpzt94gk9v/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1304758 1313436 + 1 chr1 1757834 1760660 - 1 chr1 4030315 4039498 - 1 chr1 9150208 9155029 - 1 chr11 5197855 5206693 - 1 chr16 2 4365 - 1 chr18 618317 624649 - 1 chr20 9654994 9655992 - 1 chr4 4413951 4417862 - 1 chr9 5143949 5149257 - 1 chrY 613201 621729 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1304758 1313436 1 1 chr1 1757834 1760660 1 2 chr1 4030315 4039498 1 3 chr1 9150208 9155029 1 4 chr11 5197855 5206693 1 5 chr16 2 4365 1 6 chr18 618317 624649 1 7 chr20 9654994 9655992 1 8 chr4 4413951 4417862 1 9 chr9 5143949 5149257 1 10 chrY 613201 621729 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr6 | 4831657 | 4831658 | a | 0 | + | | chr13 | 2245169 | 2252951 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpltbbunkl/f1.bed) resultresultresultresultresultresultresultresultresultresult chr13 2245169 2252951 + 1 chr6 4831657 4831658 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr13 2245169 2252951 1 1 chr6 4831657 4831658 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4519671 | 4521922 | a | 0 | - | | chr1 | 4189005 | 4189151 | a | 0 | - | | chr1 | 2475476 | 2476960 | a | 0 | - | | chr6 | 3687905 | 3689389 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr12 | 1803327 | 1812461 | a | 0 | + | | chr12 | 2 | 1486 | a | 0 | + | | chr12 | 8005421 | 8005422 | a | 0 | + | | chr12 | 154862 | 160065 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp867npchz/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2475476 2476960 - 1 chr1 4189005 4189151 - 1 chr1 4519671 4521922 - 1 chr12 2 1486 + 1 chr12 154862 160065 - 1 chr12 1803327 1812461 + 1 chr12 4914089 4922094 + 1 chr12 8005421 8005422 + 1 chr12 9832761 9838660 + 1 chr12 9983705 9985189 + 1 chr6 3687905 3689389 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 2475476 2476960 1 1 chr1 4189005 4189151 1 2 chr1 4519671 4521922 1 3 chr12 2 1486 1 4 chr12 154862 160065 1 5 chr12 1803327 1812461 1 6 chr12 4914089 4922094 1 7 chr12 8005421 8005422 1 8 chr12 9832761 9838660 1 9 chr12 9983705 9985189 1 10 chr6 3687905 3689389 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 117594 | 122968 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpjcbp1y3v/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 117594 122968 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 117594 122968 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chrX | 8814841 | 8824411 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpkj8k8cjv/f1.bed) resultresultresultresultresultresultresultresultresultresult chrX 8814841 8824411 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chrX 8814841 8824411 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8774743 | 8777326 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp9kil7d3_/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 8774743 8777326 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 8774743 8777326 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3846168 | 3849340 | a | 0 | + | | chr7 | 4699547 | 4703619 | a | 0 | + | | chr13 | 1840512 | 1849540 | a | 0 | - | | chr16 | 5219125 | 5223756 | a | 0 | + | | chr17 | 3878670 | 3879969 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpu5jmb98l/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 3846168 3849340 + 1 chr13 1840512 1849540 - 1 chr16 5219125 5223756 + 1 chr17 3878670 3879969 - 1 chr7 4699547 4703619 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 3846168 3849340 1 1 chr13 1840512 1849540 1 2 chr16 5219125 5223756 1 3 chr17 3878670 3879969 1 4 chr7 4699547 4703619 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr10 | 280026 | 280752 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpyd_lpgw0/f1.bed) resultresultresultresultresultresultresultresultresultresult chr10 280026 280752 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr10 280026 280752 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5813863 | 5818631 | a | 0 | + | | chr7 | 6806883 | 6812050 | a | 0 | - | | chr20 | 8817496 | 8826588 | a | 0 | - | | chr22 | 1 | 5330 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp9srozcum/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 5813863 5818631 + 1 chr20 8817496 8826588 - 1 chr22 1 5330 - 1 chr7 6806883 6812050 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 5813863 5818631 1 1 chr20 8817496 8826588 1 2 chr22 1 5330 1 3 chr7 6806883 6812050 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1748071 | 1754352 | a | 0 | + | | chr1 | 1748071 | 1753069 | a | 0 | + | | chr1 | 1748071 | 1748072 | a | 0 | - | | chr11 | 1748071 | 1749702 | a | 0 | + | | chrY | 3351074 | 3351076 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpp29qn7et/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1748071 1754352 - 3 chr11 1748071 1749702 + 1 chrY 3351074 3351076 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1748071 1754352 3 1 chr11 1748071 1749702 1 2 chrY 3351074 3351076 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9747561 | 9756152 | a | 0 | - | | chr1 | 413353 | 417626 | a | 0 | - | | chr1 | 5273051 | 5282974 | a | 0 | - | | chr1 | 313769 | 323675 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr18 | 1062579 | 1063172 | a | 0 | + | | chr21 | 10000000 | 10006872 | a | 0 | + | | chr21 | 9718882 | 9728882 | a | 0 | + | | chrY | 1563506 | 1564099 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmps_e9cdw3/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 313769 323675 - 1 chr1 413353 417626 - 1 chr1 5273051 5282974 - 1 chr1 9747561 9756152 - 1 chr14 3835138 3841152 + 1 chr18 1062579 1063172 + 1 chr21 9718882 9728882 + 1 chr21 10000000 10006872 + 1 chr5 2658606 2662934 - 1 chr5 9964000 9964311 + 1 chrY 1563506 1564099 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 313769 323675 1 1 chr1 413353 417626 1 2 chr1 5273051 5282974 1 3 chr1 9747561 9756152 1 4 chr14 3835138 3841152 1 5 chr18 1062579 1063172 1 6 chr21 9718882 9728882 1 7 chr21 10000000 10006872 1 8 chr5 2658606 2662934 1 9 chr5 9964000 9964311 1 10 chrY 1563506 1564099 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9246337 | 9249330 | a | 0 | - | | chr4 | 8996094 | 9003632 | a | 0 | - | | chr14 | 2055933 | 2058269 | a | 0 | + | | chr17 | 804493 | 804495 | a | 0 | + | | chr17 | 8881530 | 8884523 | a | 0 | + | | chr19 | 4931134 | 4941017 | a | 0 | + | | chr22 | 6522302 | 6527087 | a | 0 | + | | chrX | 7581542 | 7586919 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 8 rows and 6 columns from 7 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmptmwtkghi/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 9246337 9249330 - 1 chr14 2055933 2058269 + 1 chr17 804493 804495 + 1 chr17 8881530 8884523 + 1 chr19 4931134 4941017 + 1 chr22 6522302 6527087 + 1 chr4 8996094 9003632 - 1 chrX 7581542 7586919 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 9246337 9249330 1 1 chr14 2055933 2058269 1 2 chr17 804493 804495 1 3 chr17 8881530 8884523 1 4 chr19 4931134 4941017 1 5 chr22 6522302 6527087 1 6 chr4 8996094 9003632 1 7 chrX 7581542 7586919 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9473479 | 9478249 | a | 0 | + | | chr1 | 718866 | 723115 | a | 0 | + | | chr1 | 2540584 | 2545533 | a | 0 | - | | chr1 | 9717497 | 9720101 | a | 0 | - | | chr1 | 1948184 | 1951372 | a | 0 | - | | chr8 | 8509945 | 8509946 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp_u1qp7dm/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 718866 723115 + 1 chr1 1948184 1951372 - 1 chr1 2540584 2545533 - 1 chr1 9473479 9478249 + 1 chr1 9717497 9720101 - 1 chr8 8509945 8509946 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 718866 723115 1 1 chr1 1948184 1951372 1 2 chr1 2540584 2545533 1 3 chr1 9473479 9478249 1 4 chr1 9717497 9720101 1 5 chr8 8509945 8509946 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6881490 | 6889054 | a | 0 | - | | chr1 | 6177984 | 6187555 | a | 0 | - | | chr13 | 7501152 | 7509024 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpb6uuuftx/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 6177984 6187555 - 1 chr1 6881490 6889054 - 1 chr13 7501152 7509024 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 6177984 6187555 1 1 chr1 6881490 6889054 1 2 chr13 7501152 7509024 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7359294 | 7359424 | a | 0 | + | | chr1 | 6557380 | 6557510 | a | 0 | + | | chr1 | 6796344 | 6806344 | a | 0 | - | | chr1 | 6796344 | 6796474 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr10 | 6796344 | 6798546 | a | 0 | - | | chr11 | 6796344 | 6804578 | a | 0 | - | | chr18 | 2498311 | 2502292 | a | 0 | + | | chr22 | 6796344 | 6803206 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 10 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp8hth2l1m/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 3628286 3628984 - 1 chr1 6557380 6557510 + 1 chr1 6796344 6806344 - 2 chr1 7359294 7359424 + 1 chr10 6796344 6798546 - 1 chr11 6796344 6804578 - 1 chr18 2498311 2502292 + 1 chr22 6796344 6803206 + 1 chr5 6796344 6803101 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 3628286 3628984 1 1 chr1 6557380 6557510 1 2 chr1 6796344 6806344 2 3 chr1 7359294 7359424 1 4 chr10 6796344 6798546 1 5 chr11 6796344 6804578 1 6 chr18 2498311 2502292 1 7 chr22 6796344 6803206 1 8 chr5 6796344 6803101 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8884897 | 8885644 | a | 0 | + | | chr1 | 206498 | 216448 | a | 0 | + | | chr1 | 9090052 | 9095164 | a | 0 | - | | chr1 | 4577497 | 4578244 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr2 | 4721206 | 4721953 | a | 0 | + | | chr2 | 4322749 | 4323496 | a | 0 | + | | chr7 | 6068242 | 6068335 | a | 0 | - | | chr11 | 4463446 | 4464193 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpdew82jlz/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 206498 216448 + 1 chr1 4577497 4578244 - 1 chr1 5596919 5597666 - 1 chr1 6291394 6292141 - 1 chr1 8884897 8885644 + 1 chr1 9090052 9095164 - 1 chr1 9187991 9191383 - 1 chr11 4463446 4464193 - 1 chr2 4322749 4323496 + 1 chr2 4721206 4721953 + 1 chr7 6068242 6068335 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 206498 216448 1 1 chr1 4577497 4578244 1 2 chr1 5596919 5597666 1 3 chr1 6291394 6292141 1 4 chr1 8884897 8885644 1 5 chr1 9090052 9095164 1 6 chr1 9187991 9191383 1 7 chr11 4463446 4464193 1 8 chr2 4322749 4323496 1 9 chr2 4721206 4721953 1 10 chr7 6068242 6068335 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5692856 | 5698331 | a | 0 | + | | chr1 | 5692856 | 5692857 | a | 0 | - | | chr3 | 5692856 | 5693895 | a | 0 | - | | chr3 | 5692856 | 5695658 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr10 | 5692856 | 5702856 | a | 0 | + | | chr13 | 5692856 | 5698556 | a | 0 | - | | chr18 | 5692856 | 5697589 | a | 0 | - | | chr19 | 5692856 | 5702037 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 8 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpkdceipwu/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 5692856 5698331 - 2 chr10 5692856 5702856 + 1 chr13 5692856 5698556 - 1 chr18 5692856 5697589 - 1 chr19 5692856 5702037 + 1 chr3 5692856 5695658 - 2 chr4 5692856 5699046 - 1 chr5 5692856 5698617 + 2 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 5692856 5698331 2 1 chr10 5692856 5702856 1 2 chr13 5692856 5698556 1 3 chr18 5692856 5697589 1 4 chr19 5692856 5702037 1 5 chr3 5692856 5695658 2 6 chr4 5692856 5699046 1 7 chr5 5692856 5698617 2 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr14 | 8485421 | 8488713 | a | 0 | - | | chrY | 6375243 | 6379443 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpdyz_ro9z/f1.bed) resultresultresultresultresultresultresultresultresultresult chr14 8485421 8488713 - 1 chrY 6375243 6379443 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr14 8485421 8488713 1 1 chrY 6375243 6379443 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr4 | 5861334 | 5870969 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp5_cvu01v/f1.bed) resultresultresultresultresultresultresultresultresultresult chr4 5861334 5870969 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr4 5861334 5870969 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5849089 | 5858698 | a | 0 | + | | chr1 | 4850874 | 4853736 | a | 0 | + | | chr1 | 1665195 | 1673770 | a | 0 | + | | chr1 | 5497545 | 5498933 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr4 | 9276603 | 9284612 | a | 0 | + | | chr10 | 5993756 | 5996452 | a | 0 | + | | chr10 | 10000000 | 10006213 | a | 0 | - | | chr14 | 7211009 | 7220618 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 10 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp0529k79h/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1665195 1673770 + 1 chr1 4850874 4853736 + 1 chr1 5497545 5498933 - 1 chr1 5849089 5858698 + 1 chr10 5993756 5996452 + 1 chr10 10000000 10006213 - 1 chr14 7211009 7220618 + 1 chr2 191101 193450 - 1 chr2 1115002 1120069 - 1 chr4 9276603 9284612 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1665195 1673770 1 1 chr1 4850874 4853736 1 2 chr1 5497545 5498933 1 3 chr1 5849089 5858698 1 4 chr10 5993756 5996452 1 5 chr10 10000000 10006213 1 6 chr14 7211009 7220618 1 7 chr2 191101 193450 1 8 chr2 1115002 1120069 1 9 chr4 9276603 9284612 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chrX | 5854495 | 5861435 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmps92xtwrv/f1.bed) resultresultresultresultresultresultresultresultresultresult chrX 5854495 5861435 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chrX 5854495 5861435 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chrY | 1134888 | 1135005 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp013lsv3t/f1.bed) resultresultresultresultresultresultresultresultresultresult chrY 1134888 1135005 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chrY 1134888 1135005 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9390994 | 9392010 | a | 0 | - | | chr1 | 6700968 | 6709732 | a | 0 | - | | chr1 | 8383051 | 8384067 | a | 0 | - | | chr1 | 5593512 | 5598415 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr1 | 2 | 2779 | a | 0 | - | | chr1 | 6592922 | 6593938 | a | 0 | - | | chr1 | 3483186 | 3484202 | a | 0 | - | | chr1 | 3705962 | 3706978 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp9oavxgf9/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2 2779 - 1 chr1 3483186 3484202 - 1 chr1 3705962 3706978 - 1 chr1 5593512 5598415 - 1 chr1 6592922 6593938 - 1 chr1 6700968 6709732 - 1 chr1 8383051 8384067 - 1 chr1 9390994 9392010 - 1 chr17 8110256 8111522 - 1 chr20 4819729 4820745 - 1 chrY 7325779 7326795 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 2 2779 1 1 chr1 3483186 3484202 1 2 chr1 3705962 3706978 1 3 chr1 5593512 5598415 1 4 chr1 6592922 6593938 1 5 chr1 6700968 6709732 1 6 chr1 8383051 8384067 1 7 chr1 9390994 9392010 1 8 chr17 8110256 8111522 1 9 chr20 4819729 4820745 1 10 chrY 7325779 7326795 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3003683 | 3011746 | a | 0 | - | | chrY | 9471822 | 9474953 | a | 0 | - | | chrY | 1319937 | 1326304 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpwh6mm1bq/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 3003683 3011746 - 1 chrY 1319937 1326304 - 1 chrY 9471822 9474953 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 3003683 3011746 1 1 chrY 1319937 1326304 1 2 chrY 9471822 9474953 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6287317 | 6290155 | a | 0 | + | | chr9 | 796370 | 805949 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmph1ns4qte/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 6287317 6290155 + 1 chr9 796370 805949 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 6287317 6290155 1 1 chr9 796370 805949 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3603863 | 3612630 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpm0iwov1n/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 3603863 3612630 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 3603863 3612630 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8992676 | 9000232 | a | 0 | + | | chr1 | 8992676 | 9000886 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpqwwdf8a8/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 8992676 9000886 + 2 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 8992676 9000886 2 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1260351 | 1266633 | a | 0 | - | | chr1 | 8034238 | 8035311 | a | 0 | - | | chr1 | 7556785 | 7557017 | a | 0 | - | | chr1 | 6130505 | 6133192 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr6 | 1856801 | 1860853 | a | 0 | + | | chr19 | 7360709 | 7361903 | a | 0 | - | | chr19 | 7078432 | 7079505 | a | 0 | - | | chr22 | 6041690 | 6045931 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 10 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpsyx6zeol/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1260351 1266633 - 1 chr1 5706665 5707738 - 1 chr1 6130505 6133192 - 1 chr1 7556785 7557017 - 1 chr1 8034238 8035311 - 1 chr1 9955479 9960086 - 1 chr19 7078432 7079505 - 1 chr19 7360709 7361903 - 1 chr22 6041690 6045931 - 1 chr6 1856801 1860853 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1260351 1266633 1 1 chr1 5706665 5707738 1 2 chr1 6130505 6133192 1 3 chr1 7556785 7557017 1 4 chr1 8034238 8035311 1 5 chr1 9955479 9960086 1 6 chr19 7078432 7079505 1 7 chr19 7360709 7361903 1 8 chr22 6041690 6045931 1 9 chr6 1856801 1860853 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 34057 | 42935 | a | 0 | + | | chr1 | 34057 | 42975 | a | 0 | + | | chr1 | 34057 | 38888 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpbi4ny228/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 34057 42975 + 3 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 34057 42975 3 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4487941 | 4495289 | a | 0 | - | | chr1 | 7622194 | 7625967 | a | 0 | - | | chr1 | 10000000 | 10002958 | a | 0 | - | | chr1 | 8180875 | 8181097 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr10 | 7856699 | 7866499 | a | 0 | - | | chr11 | 2524349 | 2533669 | a | 0 | - | | chr14 | 956393 | 965359 | a | 0 | - | | chrY | 8949276 | 8951731 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 9 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpzepmc3vh/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 4487941 4495289 - 1 chr1 5970921 5975190 - 1 chr1 7622194 7625967 - 1 chr1 8180875 8181097 - 1 chr1 10000000 10002958 - 1 chr10 7856699 7866499 - 1 chr11 2524349 2533669 - 1 chr14 956393 965359 - 1 chrY 8949276 8951731 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 4487941 4495289 1 1 chr1 5970921 5975190 1 2 chr1 7622194 7625967 1 3 chr1 8180875 8181097 1 4 chr1 10000000 10002958 1 5 chr10 7856699 7866499 1 6 chr11 2524349 2533669 1 7 chr14 956393 965359 1 8 chrY 8949276 8951731 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1825901 | 1831304 | a | 0 | + | | chr1 | 4141353 | 4147630 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp1v7dkn06/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1825901 1831304 + 1 chr1 4141353 4147630 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1825901 1831304 1 1 chr1 4141353 4147630 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6824326 | 6827794 | a | 0 | + | | chr1 | 8306966 | 8310434 | a | 0 | + | | chr1 | 9096368 | 9099836 | a | 0 | - | | chr6 | 2902264 | 2905732 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr10 | 2 | 7946 | a | 0 | + | | chr10 | 1007926 | 1011394 | a | 0 | - | | chrX | 1415801 | 1421597 | a | 0 | - | | chrX | 485150 | 488618 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpyewwvky_/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 6824326 6827794 + 1 chr1 8306966 8310434 + 1 chr1 9096368 9099836 - 1 chr10 2 7946 + 1 chr10 1007926 1011394 - 1 chr6 2902264 2905732 + 1 chr8 2627007 2630475 + 1 chr9 1949371 1952839 - 1 chrX 485150 488618 - 1 chrX 1415801 1421597 - 1 chrX 4306030 4309498 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 6824326 6827794 1 1 chr1 8306966 8310434 1 2 chr1 9096368 9099836 1 3 chr10 2 7946 1 4 chr10 1007926 1011394 1 5 chr6 2902264 2905732 1 6 chr8 2627007 2630475 1 7 chr9 1949371 1952839 1 8 chrX 485150 488618 1 9 chrX 1415801 1421597 1 10 chrX 4306030 4309498 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1897164 | 1898104 | a | 0 | + | | chr1 | 6347401 | 6352155 | a | 0 | + | | chr1 | 2744409 | 2747220 | a | 0 | + | | chr1 | 7446667 | 7447238 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr1 | 7347438 | 7348459 | a | 0 | - | | chr1 | 3379710 | 3382197 | a | 0 | - | | chr1 | 3782685 | 3789865 | a | 0 | - | | chr1 | 4173035 | 4173036 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp02mbaldz/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1897164 1898104 + 1 chr1 2744409 2747220 + 1 chr1 3379710 3382197 - 1 chr1 3782685 3789865 - 1 chr1 4173035 4173036 - 1 chr1 6347401 6352155 + 1 chr1 7347438 7348459 - 1 chr1 7446667 7447238 + 1 chr17 5237560 5247191 + 1 chr20 4777801 4787070 - 1 chr21 10000000 10009842 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1897164 1898104 1 1 chr1 2744409 2747220 1 2 chr1 3379710 3382197 1 3 chr1 3782685 3789865 1 4 chr1 4173035 4173036 1 5 chr1 6347401 6352155 1 6 chr1 7347438 7348459 1 7 chr1 7446667 7447238 1 8 chr17 5237560 5247191 1 9 chr20 4777801 4787070 1 10 chr21 10000000 10009842 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr22 | 3047217 | 3055739 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpnyutppt0/f1.bed) resultresultresultresultresultresultresultresultresultresult chr22 3047217 3055739 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr22 3047217 3055739 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 10000000 | 10007170 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpv6ko7u0p/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 10000000 10007170 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 10000000 10007170 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9587955 | 9596101 | a | 0 | + | | chr1 | 9670698 | 9672284 | a | 0 | - | | chr1 | 9999999 | 10007070 | a | 0 | - | | chr1 | 3369009 | 3369010 | a | 0 | - | | chr1 | 804630 | 813650 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp1ukodg0m/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 804630 813650 - 1 chr1 3369009 3369010 - 1 chr1 9587955 9596101 + 1 chr1 9670698 9672284 - 1 chr1 9999999 10007070 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 804630 813650 1 1 chr1 3369009 3369010 1 2 chr1 9587955 9596101 1 3 chr1 9670698 9672284 1 4 chr1 9999999 10007070 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2120450 | 2126956 | a | 0 | + | | chr1 | 3527205 | 3532158 | a | 0 | + | | chr1 | 5413164 | 5418117 | a | 0 | + | | chr4 | 697363 | 705735 | a | 0 | + | | chr10 | 3099343 | 3108160 | a | 0 | + | | chr20 | 5413164 | 5420053 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpdvudi51f/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2120450 2126956 + 1 chr1 3527205 3532158 + 1 chr1 5413164 5418117 + 1 chr10 3099343 3108160 + 1 chr20 5413164 5420053 + 1 chr4 697363 705735 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 2120450 2126956 1 1 chr1 3527205 3532158 1 2 chr1 5413164 5418117 1 3 chr10 3099343 3108160 1 4 chr20 5413164 5420053 1 5 chr4 697363 705735 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4275653 | 4283871 | a | 0 | + | | chr1 | 9164631 | 9172604 | a | 0 | - | | chr1 | 1337477 | 1338265 | a | 0 | - | | chr1 | 6627063 | 6627241 | a | 0 | - | | chr1 | 9558980 | 9566419 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmplv1caubd/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1337477 1338265 - 1 chr1 4275653 4283871 + 1 chr1 6627063 6627241 - 1 chr1 9164631 9172604 - 1 chr1 9558980 9566419 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1337477 1338265 1 1 chr1 4275653 4283871 1 2 chr1 6627063 6627241 1 3 chr1 9164631 9172604 1 4 chr1 9558980 9566419 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3986210 | 3990128 | a | 0 | - | | chr1 | 3986210 | 3991692 | a | 0 | - | | chr1 | 5568924 | 5572343 | a | 0 | - | | chr1 | 3986210 | 3994432 | a | 0 | - | | chr4 | 3986210 | 3991017 | a | 0 | + | | chr8 | 3986210 | 3991017 | a | 0 | - | | chr13 | 3986210 | 3988434 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 7 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp3x3883dz/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 3986210 3994432 - 3 chr1 5568924 5572343 - 1 chr13 3986210 3988434 + 1 chr4 3986210 3991017 + 1 chr8 3986210 3991017 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 3986210 3994432 3 1 chr1 5568924 5572343 1 2 chr13 3986210 3988434 1 3 chr4 3986210 3991017 1 4 chr8 3986210 3991017 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9795888 | 9800359 | a | 0 | + | | chr1 | 9240176 | 9249939 | a | 0 | - | | chr1 | 6472311 | 6477768 | a | 0 | - | | chr4 | 9240176 | 9243451 | a | 0 | - | | chr7 | 4733824 | 4735764 | a | 0 | + | | chr16 | 3723976 | 3728936 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpt9p7cpl4/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 6472311 6477768 - 1 chr1 9240176 9249939 - 1 chr1 9795888 9800359 + 1 chr16 3723976 3728936 - 1 chr4 9240176 9243451 - 1 chr7 4733824 4735764 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 6472311 6477768 1 1 chr1 9240176 9249939 1 2 chr1 9795888 9800359 1 3 chr16 3723976 3728936 1 4 chr4 9240176 9243451 1 5 chr7 4733824 4735764 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr7 | 9174908 | 9177482 | a | 0 | + | | chr20 | 2035434 | 2043794 | a | 0 | + | | chr22 | 8856121 | 8865408 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp8bhamyhm/f1.bed) resultresultresultresultresultresultresultresultresultresult chr20 2035434 2043794 + 1 chr22 8856121 8865408 - 1 chr7 9174908 9177482 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr20 2035434 2043794 1 1 chr22 8856121 8865408 1 2 chr7 9174908 9177482 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 954226 | 958351 | a | 0 | + | | chr1 | 1246979 | 1256672 | a | 0 | + | | chr1 | 3466733 | 3471449 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp42_bonrh/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 954226 958351 + 1 chr1 1246979 1256672 + 1 chr1 3466733 3471449 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 954226 958351 1 1 chr1 1246979 1256672 1 2 chr1 3466733 3471449 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7562210 | 7571585 | a | 0 | + | | chr1 | 4029804 | 4037802 | a | 0 | + | | chr1 | 9426136 | 9434134 | a | 0 | - | | chr1 | 375494 | 381467 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr12 | 8578357 | 8585971 | a | 0 | - | | chr16 | 375494 | 381927 | a | 0 | + | | chr22 | 6032290 | 6042176 | a | 0 | - | | chrM | 9999999 | 10003877 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 7 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpyvi6f1gd/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 375494 381467 - 1 chr1 4029804 4037802 + 1 chr1 4323322 4331320 - 1 chr1 7562210 7571585 + 1 chr1 9426136 9434134 - 1 chr12 8578357 8585971 - 1 chr16 375494 381927 + 1 chr22 6032290 6042176 - 1 chr5 740649 746623 - 1 chr7 2 5556 - 1 chrM 9999999 10003877 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 375494 381467 1 1 chr1 4029804 4037802 1 2 chr1 4323322 4331320 1 3 chr1 7562210 7571585 1 4 chr1 9426136 9434134 1 5 chr12 8578357 8585971 1 6 chr16 375494 381927 1 7 chr22 6032290 6042176 1 8 chr5 740649 746623 1 9 chr7 2 5556 1 10 chrM 9999999 10003877 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1105475 | 1111192 | a | 0 | + | | chr1 | 1105475 | 1113008 | a | 0 | + | | chr1 | 1800656 | 1804438 | a | 0 | + | | chr1 | 8802917 | 8808634 | a | 0 | - | | chr1 | 5625181 | 5634294 | a | 0 | - | | chr4 | 8309991 | 8315708 | a | 0 | + | | chr4 | 5295705 | 5297281 | a | 0 | - | | chr16 | 4488051 | 4494160 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 8 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmptoc0pvzk/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1105475 1113008 + 2 chr1 1800656 1804438 + 1 chr1 5625181 5634294 - 1 chr1 8802917 8808634 - 1 chr16 4488051 4494160 - 1 chr4 5295705 5297281 - 1 chr4 8309991 8315708 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1105475 1113008 2 1 chr1 1800656 1804438 1 2 chr1 5625181 5634294 1 3 chr1 8802917 8808634 1 4 chr16 4488051 4494160 1 5 chr4 5295705 5297281 1 6 chr4 8309991 8315708 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8025152 | 8030889 | a | 0 | - | | chrY | 2203643 | 2209380 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpms1gnymu/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 8025152 8030889 - 1 chrY 2203643 2209380 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 8025152 8030889 1 1 chrY 2203643 2209380 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1312761 | 1314973 | a | 0 | - | | chr16 | 1435970 | 1441040 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpgctlpjv0/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1312761 1314973 - 1 chr16 1435970 1441040 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1312761 1314973 1 1 chr16 1435970 1441040 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6954703 | 6958145 | a | 0 | + | | chr20 | 9999999 | 10000455 | a | 0 | + | | chr20 | 3468115 | 3473085 | a | 0 | + | | chr20 | 9293801 | 9294257 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr20 | 3946861 | 3952927 | a | 0 | + | | chr20 | 2474533 | 2482453 | a | 0 | - | | chr20 | 8598180 | 8600442 | a | 0 | - | | chr20 | 3805897 | 3809292 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpfflkiq8m/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 6954703 6958145 + 1 chr20 1076308 1082641 + 1 chr20 2474533 2482453 - 1 chr20 3468115 3473085 + 1 chr20 3805897 3809292 - 1 chr20 3946861 3952927 + 1 chr20 4724987 4726316 + 1 chr20 7001967 7010507 + 1 chr20 8598180 8600442 - 1 chr20 9293801 9294257 + 1 chr20 9999999 10000455 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 6954703 6958145 1 1 chr20 1076308 1082641 1 2 chr20 2474533 2482453 1 3 chr20 3468115 3473085 1 4 chr20 3805897 3809292 1 5 chr20 3946861 3952927 1 6 chr20 4724987 4726316 1 7 chr20 7001967 7010507 1 8 chr20 8598180 8600442 1 9 chr20 9293801 9294257 1 10 chr20 9999999 10000455 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr4 | 7858078 | 7866261 | a | 0 | - | | chr7 | 8269504 | 8277687 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp4s5blmvj/f1.bed) resultresultresultresultresultresultresultresultresultresult chr4 7858078 7866261 - 1 chr7 8269504 8277687 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr4 7858078 7866261 1 1 chr7 8269504 8277687 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 5052 | a | 0 | + | | chr1 | 5460042 | 5465741 | a | 0 | + | | chr1 | 10000000 | 10001944 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpg4swujgm/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 5052 + 1 chr1 5460042 5465741 + 1 chr1 10000000 10001944 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1 5052 1 1 chr1 5460042 5465741 1 2 chr1 10000000 10001944 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7029490 | 7039490 | a | 0 | + | | chr1 | 8477927 | 8483502 | a | 0 | - | | chr10 | 1239954 | 1240811 | a | 0 | + | | chr10 | 1 | 2785 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr10 | 1239954 | 1240811 | a | 0 | + | | chr10 | 1 | 2785 | a | 0 | + | | chr10 | 3248864 | 3255077 | a | 0 | + | | chr10 | 434875 | 438490 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 9 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpmtcm5iad/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 7029490 7039490 + 1 chr1 8477927 8483502 - 1 chr10 1 2785 + 1 chr10 434875 438490 - 1 chr10 1239954 1240811 + 1 chr10 3248864 3255077 + 1 chr12 4827225 4836509 - 1 chr14 3273667 3279256 - 1 chr21 3395457 3399516 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 7029490 7039490 1 1 chr1 8477927 8483502 1 2 chr10 1 2785 1 3 chr10 434875 438490 1 4 chr10 1239954 1240811 1 5 chr10 3248864 3255077 1 6 chr12 4827225 4836509 1 7 chr14 3273667 3279256 1 8 chr21 3395457 3399516 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3335753 | 3336178 | a | 0 | - | | chr1 | 8765043 | 8766601 | a | 0 | - | | chr6 | 496815 | 504035 | a | 0 | - | | chr10 | 1047021 | 1052215 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr12 | 2405950 | 2413527 | a | 0 | - | | chr13 | 4069711 | 4077191 | a | 0 | + | | chr17 | 2154399 | 2163523 | a | 0 | - | | chrM | 573636 | 581927 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 8 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp5mtk8kd5/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 3335753 3336178 - 1 chr1 8765043 8766601 - 1 chr10 1047021 1052215 - 1 chr11 127979 131768 + 1 chr11 4077092 4080513 - 1 chr11 7960764 7969403 + 1 chr12 2405950 2413527 - 1 chr13 4069711 4077191 + 1 chr17 2154399 2163523 - 1 chr6 496815 504035 - 1 chrM 573636 581927 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 3335753 3336178 1 1 chr1 8765043 8766601 1 2 chr10 1047021 1052215 1 3 chr11 127979 131768 1 4 chr11 4077092 4080513 1 5 chr11 7960764 7969403 1 6 chr12 2405950 2413527 1 7 chr13 4069711 4077191 1 8 chr17 2154399 2163523 1 9 chr6 496815 504035 1 10 chrM 573636 581927 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2406393 | 2407929 | a | 0 | - | | chr1 | 2406393 | 2410774 | a | 0 | - | | chr1 | 7329114 | 7330650 | a | 0 | - | | chr10 | 2406393 | 2411816 | a | 0 | + | | chr19 | 2431870 | 2438950 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp_4gjn8w5/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2406393 2410774 - 2 chr1 7329114 7330650 - 1 chr10 2406393 2411816 + 1 chr19 2431870 2438950 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 2406393 2410774 2 1 chr1 7329114 7330650 1 2 chr10 2406393 2411816 1 3 chr19 2431870 2438950 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpwjlkblwn/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1 2 1 __________ test_three_in_a_row[strandedness_chain439-method_chain439] __________ [gw7] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', None), method_chain = ('join', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('join', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:15 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:145 E (and 24 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 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PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') __________ test_three_in_a_row[strandedness_chain418-method_chain418] __________ [gw1] linux -- Python 3.12.6 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 880, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1722, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=('opposite', None), | method_chain=('nearest', 'subtract'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=Empty PyRanges, | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:73 | (and 27 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2TABIxIFCOUySijxHnGXL6TAQAJBQH5') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 4384, in subtract | other_clusters = other.merge(strand=strand) | ^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 381, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=('opposite', None), | method_chain=('nearest', 'subtract'), | gr=Empty PyRanges, | gr2=Empty PyRanges, | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:15 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:369 | (and 24 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAEECwEAAFEAAw==') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 93 | 350 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 258 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain429-method_chain429] __________ [gw0] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', None), method_chain = ('subtract', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('subtract', 'overlap'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:30 E /usr/lib/python3/dist-packages/pandas/core/dtypes/missing.py:207 E (and 18 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') __________ test_three_in_a_row[strandedness_chain417-method_chain417] __________ [gw2] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', None), method_chain = ('nearest', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('nearest', 'intersect'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:53 E (and 28 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2SAAkY4gaBhXDATzgEAAPwACA==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain434-method_chain434] __________ [gw4] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', None), method_chain = ('join', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('join', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:33 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/helpers.py:39 E (and 276 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') __________ test_three_in_a_row[strandedness_chain433-method_chain433] __________ [gw6] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', None), method_chain = ('subtract', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('subtract', 'join'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:30 E (and 19 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +6 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 11 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 6 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') __________ test_three_in_a_row[strandedness_chain432-method_chain432] __________ [gw10] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', None), method_chain = ('subtract', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('subtract', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:30 E /usr/lib/python3/dist-packages/pandas/core/dtypes/missing.py:207 E (and 19 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BAAEYUCgwAAD4AAw==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr15 | 6680 | 6681 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr17 | 6098610 | 6105290 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr17 | 6680 | 6681 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr17 | 6098610 | 6098611 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr15 | 6680 | 6681 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr17 | 6680 | 6681 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') __________ test_three_in_a_row[strandedness_chain431-method_chain431] __________ [gw9] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', None) method_chain = ('subtract', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('subtract', 'intersect'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:30 E /usr/lib/python3/dist-packages/pandas/core/dtypes/missing.py:207 E (and 18 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') _________________________________ test_windows _________________________________ [gw7] linux -- Python 3.12.6 /usr/bin/python3.12 def test_windows(): f1 = pr.data.f1() print(f1) > result = f1.tile(2) tests/windows/test_windows.py:25: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ pyranges/pyranges.py:4649: in tile df = pyrange_apply_single(_tiles, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/windows.py:40: in _tiles idxs, starts, ends = maketiles(df.index.values, df.Start.values, sorted_nearest/src/tiles.pyx:24: in sorted_nearest.src.tiles.maketiles ??? _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'long' but got 'long long' sorted_nearest/src/tiles.pyx:48: ValueError ----------------------------- Captured stdout call ----------------------------- +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int32) | (int32) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3 | 6 | interval1 | 0 | + | | chr1 | 8 | 9 | interval3 | 0 | + | | chr1 | 5 | 7 | interval2 | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. __________ test_three_in_a_row[strandedness_chain430-method_chain430] __________ [gw3] linux -- Python 3.12.6 /usr/bin/python3.12 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 880, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1722, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 292, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=('opposite', None), | method_chain=('subtract', 'nearest'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=Empty PyRanges, | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:108 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:111 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:114 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:121 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/nearest.py:73 | (and 27 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2TACxiRKCgbAACKAAU=') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 4384, in subtract | other_clusters = other.merge(strand=strand) | ^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 347, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=('opposite', None), | method_chain=('subtract', 'nearest'), | gr=Empty PyRanges, | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=Empty PyRanges, # or any other generated value | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:143 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:30 | (and 19 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr2 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 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PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 258 | a | 0 | ... | | chr1 | 1 | 258 | a | 0 | ... | | chr1 | 1 | 258 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ______________________________ test_cluster[True] ______________________________ [gw0] linux -- Python 3.12.6 /usr/bin/python3.12 strand = True @pytest.mark.bedtools > @pytest.mark.parametrize("strand", [True, False]) tests/test_unary.py:96: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_unary.py:132: in test_cluster result = gr.cluster(strand=strand) pyranges/pyranges.py:1070: in cluster df = pyrange_apply_single(_cluster, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/cluster.py:14: in _cluster ids = annotate_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_cluster( E strand=True, E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., # or any other generated value E ) sorted_nearest/src/annotate_clusters.pyx:15: Exception ----------------------------- Captured stdout call ----------------------------- +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpiuzysgoi/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 2 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3847163 | 3850872 | a | 0 | + | | chr1 | 2520070 | 2523779 | a | 0 | + | | chr1 | 4932280 | 4932893 | a | 0 | + | | chr1 | 7649464 | 7653173 | a | 0 | + | | chr1 | 3750593 | 3754302 | a | 0 | - | | chr1 | 2936890 | 2946568 | a | 0 | - | | chr1 | 4571891 | 4575600 | a | 0 | - | | chrM | 4311219 | 4314928 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 8 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpsrxg14yp/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2520070 2523779 a 0 + 1 1 chr1 3847163 3850872 a 0 + 2 2 chr1 4932280 4932893 a 0 + 3 3 chr1 7649464 7653173 a 0 + 4 4 chr1 2936890 2946568 a 0 - 5 5 chr1 3750593 3754302 a 0 - 6 6 chr1 4571891 4575600 a 0 - 7 7 chrM 4311219 4314928 a 0 + 8 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3847163 | 3850872 | a | 0 | + | | chr1 | 2520070 | 2523779 | a | 0 | + | | chr1 | 4932280 | 4932893 | a | 0 | + | | chr1 | 7649464 | 7653173 | a | 0 | + | | chr1 | 3750593 | 3754302 | a | 0 | - | | chr1 | 2936890 | 2946568 | a | 0 | - | | chr1 | 4571891 | 4575600 | a | 0 | - | | chrM | 4311219 | 4314928 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 8 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 65537 | 65794 | a | 0 | - | | chr1 | 65537 | 65794 | a | 0 | - | | chr1 | 3 | 260 | a | 0 | - | | chr1 | 65537 | 65794 | a | 0 | - | | chr1 | 65537 | 65794 | a | 0 | - | | chr1 | 65537 | 65538 | a | 0 | - | | chr2 | 65537 | 65538 | a | 0 | - | | chr2 | 2 | 259 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 8 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpa5vlqaf6/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 3 260 a 0 - 1 1 chr1 65537 65538 a 0 - 2 2 chr1 65537 65794 a 0 - 2 3 chr1 65537 65794 a 0 - 2 4 chr1 65537 65794 a 0 - 2 5 chr1 65537 65794 a 0 - 2 6 chr2 2 259 a 0 - 3 7 chr2 65537 65538 a 0 - 4 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 65537 | 65794 | a | 0 | - | | chr1 | 65537 | 65794 | a | 0 | - | | chr1 | 3 | 260 | a | 0 | - | | chr1 | 65537 | 65794 | a | 0 | - | | chr1 | 65537 | 65794 | a | 0 | - | | chr1 | 65537 | 65538 | a | 0 | - | | chr2 | 65537 | 65538 | a | 0 | - | | chr2 | 2 | 259 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 8 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 65537 | 65538 | a | 0 | - | | chr1 | 65537 | 65794 | a | 0 | - | | chr1 | 2 | 259 | a | 0 | - | | chr1 | 65537 | 65794 | a | 0 | - | | chr1 | 3 | 260 | a | 0 | - | | chr1 | 65537 | 65794 | a | 0 | - | | chr1 | 65537 | 65794 | a | 0 | - | | chr1 | 65537 | 65538 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 8 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpx3uk4yc5/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2 259 a 0 - 1 1 chr1 3 260 a 0 - 1 2 chr1 65537 65538 a 0 - 2 3 chr1 65537 65538 a 0 - 2 4 chr1 65537 65794 a 0 - 2 5 chr1 65537 65794 a 0 - 2 6 chr1 65537 65794 a 0 - 2 7 chr1 65537 65794 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 65537 | 65538 | a | 0 | - | | chr1 | 65537 | 65794 | a | 0 | - | | chr1 | 2 | 259 | a | 0 | - | | chr1 | 65537 | 65794 | a | 0 | - | | chr1 | 3 | 260 | a | 0 | - | | chr1 | 65537 | 65794 | a | 0 | - | | chr1 | 65537 | 65794 | a | 0 | - | | chr1 | 65537 | 65538 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 8 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 65537 | 65538 | a | 0 | - | | chr1 | 65537 | 65794 | a | 0 | - | | chr1 | 2 | 259 | a | 0 | - | | chr1 | 65537 | 65794 | a | 0 | - | | chr1 | 3 | 260 | a | 0 | - | | chr1 | 65537 | 65794 | a | 0 | - | | chr1 | 65537 | 65794 | a | 0 | - | | chr1 | 65537 | 65538 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 8 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpm6kvgwb8/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2 259 a 0 - 1 1 chr1 3 260 a 0 - 1 2 chr1 65537 65538 a 0 - 2 3 chr1 65537 65538 a 0 - 2 4 chr1 65537 65794 a 0 - 2 5 chr1 65537 65794 a 0 - 2 6 chr1 65537 65794 a 0 - 2 7 chr1 65537 65794 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 65537 | 65538 | a | 0 | - | | chr1 | 65537 | 65794 | a | 0 | - | | chr1 | 2 | 259 | a | 0 | - | | chr1 | 65537 | 65794 | a | 0 | - | | chr1 | 3 | 260 | a | 0 | - | | chr1 | 65537 | 65794 | a | 0 | - | | chr1 | 65537 | 65794 | a | 0 | - | | chr1 | 65537 | 65538 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 8 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 65537 | 65538 | a | 0 | - | | chr1 | 65537 | 65794 | a | 0 | - | | chr1 | 2 | 259 | a | 0 | - | | chr1 | 65537 | 65794 | a | 0 | - | | chr1 | 3 | 260 | a | 0 | - | | chr1 | 65537 | 65794 | a | 0 | - | | chr1 | 65537 | 65794 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 7 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmplpu56_kg/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2 259 a 0 - 1 1 chr1 3 260 a 0 - 1 2 chr1 65537 65538 a 0 - 2 3 chr1 65537 65794 a 0 - 2 4 chr1 65537 65794 a 0 - 2 5 chr1 65537 65794 a 0 - 2 6 chr1 65537 65794 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 65537 | 65538 | a | 0 | - | | chr1 | 65537 | 65794 | a | 0 | - | | chr1 | 2 | 259 | a | 0 | - | | chr1 | 65537 | 65794 | a | 0 | - | | chr1 | 3 | 260 | a | 0 | - | | chr1 | 65537 | 65794 | a | 0 | - | | chr1 | 65537 | 65794 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 7 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 65537 | 65794 | a | 0 | - | | chr1 | 65537 | 65794 | a | 0 | - | | chr1 | 2 | 4 | a | 0 | - | | chr1 | 65537 | 65794 | a | 0 | - | | chr1 | 3 | 6 | a | 0 | - | | chr1 | 65537 | 65794 | a | 0 | - | | chr1 | 65537 | 65794 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 7 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpckkl4_n6/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2 4 a 0 - 1 1 chr1 3 6 a 0 - 1 2 chr1 65537 65794 a 0 - 2 3 chr1 65537 65794 a 0 - 2 4 chr1 65537 65794 a 0 - 2 5 chr1 65537 65794 a 0 - 2 6 chr1 65537 65794 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 65537 | 65794 | a | 0 | - | | chr1 | 65537 | 65794 | a | 0 | - | | chr1 | 2 | 4 | a | 0 | - | | chr1 | 65537 | 65794 | a | 0 | - | | chr1 | 3 | 6 | a | 0 | - | | chr1 | 65537 | 65794 | a | 0 | - | | chr1 | 65537 | 65794 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 7 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 257 | 514 | a | 0 | - | | chr1 | 3 | 260 | a | 0 | - | | chr1 | 1 | 3 | a | 0 | - | | chr1 | 257 | 514 | a | 0 | - | | chr1 | 257 | 260 | a | 0 | - | | chr1 | 257 | 514 | a | 0 | - | | chr1 | 257 | 514 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 7 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp7parew9o/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 3 a 0 - 1 1 chr1 3 260 a 0 - 1 2 chr1 257 260 a 0 - 1 3 chr1 257 514 a 0 - 1 4 chr1 257 514 a 0 - 1 5 chr1 257 514 a 0 - 1 6 chr1 257 514 a 0 - 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 257 | 514 | a | 0 | - | | chr1 | 3 | 260 | a | 0 | - | | chr1 | 1 | 3 | a | 0 | - | | chr1 | 257 | 514 | a | 0 | - | | chr1 | 257 | 260 | a | 0 | - | | chr1 | 257 | 514 | a | 0 | - | | chr1 | 257 | 514 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 7 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1668700 | 1671887 | a | 0 | + | | chr1 | 8229443 | 8235167 | a | 0 | + | | chr1 | 8544855 | 8553432 | a | 0 | + | | chr1 | 6210248 | 6211903 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr3 | 9999999 | 10009653 | a | 0 | + | | chr8 | 1711900 | 1715708 | a | 0 | + | | chr10 | 7022524 | 7028030 | a | 0 | - | | chr13 | 8995612 | 8999340 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpd4o87dpp/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1668700 1671887 a 0 + 1 1 chr1 8229443 8235167 a 0 + 2 2 chr1 8544855 8553432 a 0 + 3 3 chr1 4494175 4498362 a 0 - 4 4 chr1 6210248 6211903 a 0 - 5 5 chr1 7215355 7223304 a 0 - 6 6 chr1 7407949 7417949 a 0 - 7 7 chr10 7022524 7028030 a 0 - 8 8 chr13 8995612 8999340 a 0 + 9 9 chr3 9999999 10009653 a 0 + 10 10 chr8 1711900 1715708 a 0 + 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1668700 | 1671887 | a | 0 | + | | chr1 | 8229443 | 8235167 | a | 0 | + | | chr1 | 8544855 | 8553432 | a | 0 | + | | chr1 | 6210248 | 6211903 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr3 | 9999999 | 10009653 | a | 0 | + | | chr8 | 1711900 | 1715708 | a | 0 | + | | chr10 | 7022524 | 7028030 | a | 0 | - | | chr13 | 8995612 | 8999340 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1668700 | 1671887 | a | 0 | + | | chr1 | 8229443 | 8235167 | a | 0 | + | | chr1 | 8544855 | 8553432 | a | 0 | + | | chr1 | 6210248 | 6211903 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr3 | 9999999 | 10009653 | a | 0 | + | | chr8 | 1711900 | 1715708 | a | 0 | + | | chr10 | 7022524 | 7028030 | a | 0 | + | | chr13 | 8995612 | 8999340 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpl8erezgx/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1668700 1671887 a 0 + 1 1 chr1 8229443 8235167 a 0 + 2 2 chr1 8544855 8553432 a 0 + 3 3 chr1 4494175 4498362 a 0 - 4 4 chr1 6210248 6211903 a 0 - 5 5 chr1 7215355 7223304 a 0 - 6 6 chr1 7407949 7417949 a 0 - 7 7 chr10 7022524 7028030 a 0 + 8 8 chr13 8995612 8999340 a 0 + 9 9 chr3 9999999 10009653 a 0 + 10 10 chr8 1711900 1715708 a 0 + 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1668700 | 1671887 | a | 0 | + | | chr1 | 8229443 | 8235167 | a | 0 | + | | chr1 | 8544855 | 8553432 | a | 0 | + | | chr1 | 6210248 | 6211903 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr3 | 9999999 | 10009653 | a | 0 | + | | chr8 | 1711900 | 1715708 | a | 0 | + | | chr10 | 7022524 | 7028030 | a | 0 | + | | chr13 | 8995612 | 8999340 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmphoghkr19/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 2 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpl_fwn79d/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 2 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpqerx8f3z/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 2 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpewzlovy9/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 2 a 0 - 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp8w2od6z8/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 2 a 0 - 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1025614 | 1035592 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpqu6d8oop/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1025614 1035592 a 0 - 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1025614 | 1035592 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9999999 | 10004092 | a | 0 | + | | chr1 | 8446776 | 8453775 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpoy6uo283/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 9999999 10004092 a 0 + 1 1 chr1 8446776 8453775 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9999999 | 10004092 | a | 0 | + | | chr1 | 8446776 | 8453775 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5548428 | 5557812 | a | 0 | + | | chr6 | 7297240 | 7298446 | a | 0 | - | | chr14 | 5884156 | 5893133 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmphrm3loi3/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 5548428 5557812 a 0 + 1 1 chr14 5884156 5893133 a 0 + 2 2 chr6 7297240 7298446 a 0 - 3 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5548428 | 5557812 | a | 0 | + | | chr6 | 7297240 | 7298446 | a | 0 | - | | chr14 | 5884156 | 5893133 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3274669 | 3280741 | a | 0 | + | | chr1 | 8698939 | 8704463 | a | 0 | - | | chr14 | 6926796 | 6933552 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpzi7dvt__/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 3274669 3280741 a 0 + 1 1 chr1 8698939 8704463 a 0 - 2 2 chr14 6926796 6933552 a 0 + 3 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3274669 | 3280741 | a | 0 | + | | chr1 | 8698939 | 8704463 | a | 0 | - | | chr14 | 6926796 | 6933552 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6026429 | 6034998 | a | 0 | + | | chr1 | 8534588 | 8536272 | a | 0 | + | | chr1 | 7970271 | 7970644 | a | 0 | + | | chr1 | 5137910 | 5147866 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr1 | 8806827 | 8810497 | a | 0 | - | | chr1 | 4528629 | 4528925 | a | 0 | - | | chr1 | 6802609 | 6802833 | a | 0 | - | | chr1 | 8634531 | 8636682 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpxotzw8m5/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 6026429 6034998 a 0 + 1 1 chr1 7970271 7970644 a 0 + 2 2 chr1 8534588 8536272 a 0 + 3 3 chr1 4528629 4528925 a 0 - 4 4 chr1 5137910 5147866 a 0 - 5 5 chr1 6802609 6802833 a 0 - 6 6 chr1 8634531 8636682 a 0 - 7 7 chr1 8806827 8810497 a 0 - 8 8 chr13 5773698 5776813 a 0 + 9 9 chr13 2250724 2254331 a 0 - 10 10 chr16 9086481 9090760 a 0 + 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6026429 | 6034998 | a | 0 | + | | chr1 | 8534588 | 8536272 | a | 0 | + | | chr1 | 7970271 | 7970644 | a | 0 | + | | chr1 | 5137910 | 5147866 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr1 | 8806827 | 8810497 | a | 0 | - | | chr1 | 4528629 | 4528925 | a | 0 | - | | chr1 | 6802609 | 6802833 | a | 0 | - | | chr1 | 8634531 | 8636682 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 235564 | 245536 | a | 0 | + | | chr1 | 2815900 | 2818433 | a | 0 | + | | chr1 | 9934489 | 9938702 | a | 0 | + | | chr1 | 2313054 | 2317116 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr2 | 7923589 | 7929658 | a | 0 | + | | chr2 | 1767780 | 1770257 | a | 0 | - | | chr8 | 1443214 | 1443326 | a | 0 | - | | chr19 | 182523 | 185533 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpa8ykd_2q/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 235564 245536 a 0 + 1 1 chr1 2815900 2818433 a 0 + 2 2 chr1 9934489 9938702 a 0 + 3 3 chr1 1602616 1605626 a 0 - 4 4 chr1 2313054 2317116 a 0 - 5 5 chr1 6930368 6934006 a 0 - 6 6 chr19 182523 185533 a 0 - 7 7 chr19 3012894 3021235 a 0 - 8 8 chr2 7923589 7929658 a 0 + 9 9 chr2 1767780 1770257 a 0 - 10 10 chr8 1443214 1443326 a 0 - 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 235564 | 245536 | a | 0 | + | | chr1 | 2815900 | 2818433 | a | 0 | + | | chr1 | 9934489 | 9938702 | a | 0 | + | | chr1 | 2313054 | 2317116 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr2 | 7923589 | 7929658 | a | 0 | + | | chr2 | 1767780 | 1770257 | a | 0 | - | | chr8 | 1443214 | 1443326 | a | 0 | - | | chr19 | 182523 | 185533 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1343842 | 1346507 | a | 0 | + | | chr1 | 1343842 | 1347893 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpy3vgtsva/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1343842 1346507 a 0 + 1 1 chr1 1343842 1347893 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1343842 | 1346507 | a | 0 | + | | chr1 | 1343842 | 1347893 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr22 | 663382 | 670595 | a | 0 | + | | chr22 | 8627079 | 8630579 | a | 0 | + | | chr22 | 1667039 | 1677038 | a | 0 | + | | chr22 | 5777131 | 5782059 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr22 | 6093463 | 6094707 | a | 0 | - | | chr22 | 2796452 | 2799534 | a | 0 | - | | chr22 | 6960770 | 6963352 | a | 0 | - | | chr22 | 3230975 | 3240214 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp8j3cp6q0/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr22 663382 670595 a 0 + 1 1 chr22 1667039 1677038 a 0 + 2 2 chr22 5051892 5060375 a 0 + 3 3 chr22 5777131 5782059 a 0 + 4 4 chr22 8627079 8630579 a 0 + 5 5 chr22 2796452 2799534 a 0 - 6 6 chr22 3230975 3240214 a 0 - 7 7 chr22 5363519 5370907 a 0 - 8 8 chr22 6093463 6094707 a 0 - 9 9 chr22 6960770 6963352 a 0 - 10 10 chr22 10000000 10006921 a 0 - 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr22 | 663382 | 670595 | a | 0 | + | | chr22 | 8627079 | 8630579 | a | 0 | + | | chr22 | 1667039 | 1677038 | a | 0 | + | | chr22 | 5777131 | 5782059 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr22 | 6093463 | 6094707 | a | 0 | - | | chr22 | 2796452 | 2799534 | a | 0 | - | | chr22 | 6960770 | 6963352 | a | 0 | - | | chr22 | 3230975 | 3240214 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5731447 | 5734877 | a | 0 | + | | chr1 | 1103566 | 1108671 | a | 0 | - | | chr9 | 5731447 | 5738512 | a | 0 | + | | chr11 | 5731447 | 5737022 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp0mxuq4oq/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 5731447 5734877 a 0 + 1 1 chr1 1103566 1108671 a 0 - 2 2 chr11 5731447 5737022 a 0 - 3 3 chr9 5731447 5738512 a 0 + 4 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5731447 | 5734877 | a | 0 | + | | chr1 | 1103566 | 1108671 | a | 0 | - | | chr9 | 5731447 | 5738512 | a | 0 | + | | chr11 | 5731447 | 5737022 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1265239 | 1269019 | a | 0 | + | | chr1 | 1 | 6314 | a | 0 | + | | chr1 | 1562028 | 1571390 | a | 0 | + | | chr1 | 7684301 | 7686507 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr1 | 4375300 | 4376856 | a | 0 | - | | chr1 | 1655936 | 1664778 | a | 0 | - | | chr1 | 3220603 | 3227373 | a | 0 | - | | chr1 | 2098078 | 2100657 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpowhj_q8q/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 6314 a 0 + 1 1 chr1 1265239 1269019 a 0 + 2 2 chr1 1562028 1571390 a 0 + 3 3 chr1 1655936 1664778 a 0 - 4 4 chr1 2098078 2100657 a 0 - 5 5 chr1 3202454 3204724 a 0 - 6 6 chr1 3220603 3227373 a 0 - 7 7 chr1 4375300 4376856 a 0 - 8 8 chr1 7684301 7686507 a 0 - 9 9 chr1 9415056 9415270 a 0 - 10 10 chr1 10000000 10009189 a 0 - 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1265239 | 1269019 | a | 0 | + | | chr1 | 1 | 6314 | a | 0 | + | | chr1 | 1562028 | 1571390 | a | 0 | + | | chr1 | 7684301 | 7686507 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr1 | 4375300 | 4376856 | a | 0 | - | | chr1 | 1655936 | 1664778 | a | 0 | - | | chr1 | 3220603 | 3227373 | a | 0 | - | | chr1 | 2098078 | 2100657 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2718597 | 2719170 | a | 0 | + | | chr1 | 2718597 | 2726149 | a | 0 | + | | chr1 | 2718597 | 2726764 | a | 0 | + | | chr1 | 2718597 | 2724291 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr1 | 2718597 | 2722989 | a | 0 | - | | chr1 | 2718597 | 2726764 | a | 0 | - | | chr1 | 2718597 | 2721529 | a | 0 | - | | chr1 | 2718597 | 2724611 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpcj7f4pdd/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2718597 2719170 a 0 + 1 1 chr1 2718597 2726149 a 0 + 1 2 chr1 2718597 2726764 a 0 + 1 3 chr1 2718597 2721529 a 0 - 2 4 chr1 2718597 2722989 a 0 - 2 5 chr1 2718597 2724291 a 0 - 2 6 chr1 2718597 2724611 a 0 - 2 7 chr1 2718597 2726764 a 0 - 2 8 chr19 2718597 2719583 a 0 + 3 9 chr21 2718597 2726482 a 0 + 4 10 chr5 2718597 2721997 a 0 - 5 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2718597 | 2719170 | a | 0 | + | | chr1 | 2718597 | 2726149 | a | 0 | + | | chr1 | 2718597 | 2726764 | a | 0 | + | | chr1 | 2718597 | 2724291 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr1 | 2718597 | 2722989 | a | 0 | - | | chr1 | 2718597 | 2726764 | a | 0 | - | | chr1 | 2718597 | 2721529 | a | 0 | - | | chr1 | 2718597 | 2724611 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7313124 | 7323124 | a | 0 | + | | chr1 | 2273928 | 2274298 | a | 0 | - | | chr1 | 8194916 | 8203565 | a | 0 | - | | chr1 | 1877338 | 1885771 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr4 | 3242060 | 3247334 | a | 0 | + | | chr4 | 1623669 | 1627334 | a | 0 | - | | chr17 | 4563978 | 4570762 | a | 0 | - | | chr17 | 7011750 | 7021638 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpvnlclulu/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 7313124 7323124 a 0 + 1 1 chr1 120503 126675 a 0 - 2 2 chr1 1877338 1885771 a 0 - 3 3 chr1 2273928 2274298 a 0 - 4 4 chr1 6764953 6767435 a 0 - 5 5 chr1 8194916 8203565 a 0 - 6 6 chr1 8984802 8990176 a 0 - 7 7 chr17 4563978 4570762 a 0 - 8 8 chr17 7011750 7021638 a 0 - 9 9 chr4 3242060 3247334 a 0 + 10 10 chr4 1623669 1627334 a 0 - 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7313124 | 7323124 | a | 0 | + | | chr1 | 2273928 | 2274298 | a | 0 | - | | chr1 | 8194916 | 8203565 | a | 0 | - | | chr1 | 1877338 | 1885771 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr4 | 3242060 | 3247334 | a | 0 | + | | chr4 | 1623669 | 1627334 | a | 0 | - | | chr17 | 4563978 | 4570762 | a | 0 | - | | chr17 | 7011750 | 7021638 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1162630 | 1170629 | a | 0 | + | | chr14 | 1162630 | 1167578 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp5w28ppss/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1162630 1170629 a 0 + 1 1 chr14 1162630 1167578 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1162630 | 1170629 | a | 0 | + | | chr14 | 1162630 | 1167578 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 814491 | 817770 | a | 0 | + | | chr1 | 814491 | 818403 | a | 0 | + | | chr1 | 814491 | 820893 | a | 0 | + | | chr1 | 1136204 | 1141629 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr13 | 7919777 | 7926366 | a | 0 | + | | chr13 | 4922258 | 4931044 | a | 0 | + | | chrM | 8701252 | 8708025 | a | 0 | - | | chrM | 814491 | 821641 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpatxzj_9p/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 814491 817770 a 0 + 1 1 chr1 814491 818403 a 0 + 1 2 chr1 814491 820893 a 0 + 1 3 chr1 1136204 1141629 a 0 - 2 4 chr1 9631302 9637114 a 0 - 3 5 chr13 4922258 4931044 a 0 + 4 6 chr13 7919777 7926366 a 0 + 5 7 chr4 814491 822714 a 0 + 6 8 chrM 814491 821641 a 0 - 7 9 chrM 8701252 8708025 a 0 - 8 10 chrY 8642486 8647042 a 0 + 9 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 814491 | 817770 | a | 0 | + | | chr1 | 814491 | 818403 | a | 0 | + | | chr1 | 814491 | 820893 | a | 0 | + | | chr1 | 1136204 | 1141629 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr13 | 7919777 | 7926366 | a | 0 | + | | chr13 | 4922258 | 4931044 | a | 0 | + | | chrM | 8701252 | 8708025 | a | 0 | - | | chrM | 814491 | 821641 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr10 | 6805273 | 6805842 | a | 0 | + | | chr10 | 6022143 | 6024049 | a | 0 | + | | chr10 | 1930621 | 1939326 | a | 0 | + | | chr10 | 4299012 | 4306700 | a | 0 | + | | chr10 | 8247827 | 8249488 | a | 0 | + | | chr10 | 1047780 | 1048646 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp67wtzt5v/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr10 1930621 1939326 a 0 + 1 1 chr10 4299012 4306700 a 0 + 2 2 chr10 6022143 6024049 a 0 + 3 3 chr10 6805273 6805842 a 0 + 4 4 chr10 8247827 8249488 a 0 + 5 5 chr10 1047780 1048646 a 0 - 6 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr10 | 6805273 | 6805842 | a | 0 | + | | chr10 | 6022143 | 6024049 | a | 0 | + | | chr10 | 1930621 | 1939326 | a | 0 | + | | chr10 | 4299012 | 4306700 | a | 0 | + | | chr10 | 8247827 | 8249488 | a | 0 | + | | chr10 | 1047780 | 1048646 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr8 | 2202477 | 2203994 | a | 0 | + | | chr8 | 8868848 | 8870898 | a | 0 | + | | chr8 | 9043901 | 9045419 | a | 0 | + | | chr8 | 3473545 | 3480779 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr8 | 454467 | 463703 | a | 0 | - | | chr8 | 2 | 1299 | a | 0 | - | | chr8 | 2976705 | 2986520 | a | 0 | - | | chr8 | 674503 | 681317 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp9i0iuq4x/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr12 6833806 6833860 a 0 - 1 1 chr13 4136045 4143321 a 0 + 2 2 chr22 1041949 1050721 a 0 + 3 3 chr8 2202477 2203994 a 0 + 4 4 chr8 8868848 8870898 a 0 + 5 5 chr8 9043901 9045419 a 0 + 6 6 chr8 2 1299 a 0 - 7 7 chr8 454467 463703 a 0 - 8 8 chr8 674503 681317 a 0 - 9 9 chr8 2976705 2986520 a 0 - 10 10 chr8 3473545 3480779 a 0 - 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr8 | 2202477 | 2203994 | a | 0 | + | | chr8 | 8868848 | 8870898 | a | 0 | + | | chr8 | 9043901 | 9045419 | a | 0 | + | | chr8 | 3473545 | 3480779 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr8 | 454467 | 463703 | a | 0 | - | | chr8 | 2 | 1299 | a | 0 | - | | chr8 | 2976705 | 2986520 | a | 0 | - | | chr8 | 674503 | 681317 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6561983 | 6564359 | a | 0 | + | | chr1 | 8905567 | 8908110 | a | 0 | - | | chr3 | 9999999 | 10008456 | a | 0 | + | | chr5 | 5070825 | 5077440 | a | 0 | + | | chr10 | 817948 | 827313 | a | 0 | + | | chr15 | 10000000 | 10005613 | a | 0 | - | | chrM | 9215067 | 9220066 | a | 0 | - | | chrY | 1244495 | 1253792 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 8 rows and 6 columns from 7 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpzx9ul6sq/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 6561983 6564359 a 0 + 1 1 chr1 8905567 8908110 a 0 - 2 2 chr10 817948 827313 a 0 + 3 3 chr15 10000000 10005613 a 0 - 4 4 chr3 9999999 10008456 a 0 + 5 5 chr5 5070825 5077440 a 0 + 6 6 chrM 9215067 9220066 a 0 - 7 7 chrY 1244495 1253792 a 0 + 8 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6561983 | 6564359 | a | 0 | + | | chr1 | 8905567 | 8908110 | a | 0 | - | | chr3 | 9999999 | 10008456 | a | 0 | + | | chr5 | 5070825 | 5077440 | a | 0 | + | | chr10 | 817948 | 827313 | a | 0 | + | | chr15 | 10000000 | 10005613 | a | 0 | - | | chrM | 9215067 | 9220066 | a | 0 | - | | chrY | 1244495 | 1253792 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 8 rows and 6 columns from 7 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4633932 | 4640746 | a | 0 | + | | chr9 | 6030524 | 6032811 | a | 0 | - | | chr13 | 7683301 | 7686980 | a | 0 | - | | chr22 | 1487715 | 1497142 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmplafit5ts/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 4633932 4640746 a 0 + 1 1 chr13 7683301 7686980 a 0 - 2 2 chr22 1487715 1497142 a 0 + 3 3 chr9 6030524 6032811 a 0 - 4 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4633932 | 4640746 | a | 0 | + | | chr9 | 6030524 | 6032811 | a | 0 | - | | chr13 | 7683301 | 7686980 | a | 0 | - | | chr22 | 1487715 | 1497142 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9733737 | 9738995 | a | 0 | + | | chr1 | 1970432 | 1979536 | a | 0 | + | | chr1 | 2754824 | 2760082 | a | 0 | - | | chr1 | 8087927 | 8096454 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr2 | 6407252 | 6411415 | a | 0 | + | | chr2 | 3492422 | 3497680 | a | 0 | - | | chr12 | 489799 | 495057 | a | 0 | - | | chr22 | 2754824 | 2760082 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpn8_4ff1o/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1970432 1979536 a 0 + 1 1 chr1 9733737 9738995 a 0 + 2 2 chr1 86782 92040 a 0 - 3 3 chr1 2754824 2760082 a 0 - 4 4 chr1 6769948 6775206 a 0 - 5 5 chr1 8087927 8096454 a 0 - 6 6 chr1 9303019 9303242 a 0 - 7 7 chr12 489799 495057 a 0 - 8 8 chr2 6407252 6411415 a 0 + 9 9 chr2 3492422 3497680 a 0 - 10 10 chr22 2754824 2760082 a 0 + 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9733737 | 9738995 | a | 0 | + | | chr1 | 1970432 | 1979536 | a | 0 | + | | chr1 | 2754824 | 2760082 | a | 0 | - | | chr1 | 8087927 | 8096454 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr2 | 6407252 | 6411415 | a | 0 | + | | chr2 | 3492422 | 3497680 | a | 0 | - | | chr12 | 489799 | 495057 | a | 0 | - | | chr22 | 2754824 | 2760082 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3718979 | 3725765 | a | 0 | + | | chr1 | 315514 | 316498 | a | 0 | + | | chr1 | 315514 | 319987 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp7s_fbdp8/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 315514 316498 a 0 + 1 1 chr1 315514 319987 a 0 + 1 2 chr1 3718979 3725765 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3718979 | 3725765 | a | 0 | + | | chr1 | 315514 | 316498 | a | 0 | + | | chr1 | 315514 | 319987 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6742360 | 6746288 | a | 0 | + | | chr1 | 9972907 | 9974305 | a | 0 | + | | chr1 | 2842837 | 2851931 | a | 0 | + | | chr1 | 7450027 | 7457305 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr5 | 7641586 | 7641588 | a | 0 | + | | chr5 | 4353903 | 4361181 | a | 0 | + | | chrM | 4765639 | 4772268 | a | 0 | + | | chrX | 4466006 | 4473123 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 9 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmprfvq_ajx/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2842837 2851931 a 0 + 1 1 chr1 6742360 6746288 a 0 + 2 2 chr1 7450027 7457305 a 0 + 3 3 chr1 9972907 9974305 a 0 + 4 4 chr3 3077864 3085474 a 0 - 5 5 chr5 4353903 4361181 a 0 + 6 6 chr5 7641586 7641588 a 0 + 7 7 chrM 4765639 4772268 a 0 + 8 8 chrX 4466006 4473123 a 0 + 9 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6742360 | 6746288 | a | 0 | + | | chr1 | 9972907 | 9974305 | a | 0 | + | | chr1 | 2842837 | 2851931 | a | 0 | + | | chr1 | 7450027 | 7457305 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr5 | 7641586 | 7641588 | a | 0 | + | | chr5 | 4353903 | 4361181 | a | 0 | + | | chrM | 4765639 | 4772268 | a | 0 | + | | chrX | 4466006 | 4473123 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 9 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4386180 | 4394373 | a | 0 | + | | chr1 | 5386545 | 5390199 | a | 0 | - | | chr1 | 553277 | 555868 | a | 0 | - | | chr1 | 807948 | 811441 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr13 | 5947507 | 5950996 | a | 0 | - | | chr18 | 9282709 | 9282961 | a | 0 | - | | chr19 | 536170 | 536504 | a | 0 | - | | chr22 | 6787794 | 6788999 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp2u195w8j/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 4386180 4394373 a 0 + 1 1 chr1 553277 555868 a 0 - 2 2 chr1 807948 811441 a 0 - 3 3 chr1 5386545 5390199 a 0 - 4 4 chr1 8311647 8320893 a 0 - 5 5 chr1 9492709 9493485 a 0 - 6 6 chr10 9539200 9540397 a 0 + 7 7 chr13 5947507 5950996 a 0 - 8 8 chr18 9282709 9282961 a 0 - 9 9 chr19 536170 536504 a 0 - 10 10 chr22 6787794 6788999 a 0 - 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4386180 | 4394373 | a | 0 | + | | chr1 | 5386545 | 5390199 | a | 0 | - | | chr1 | 553277 | 555868 | a | 0 | - | | chr1 | 807948 | 811441 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr13 | 5947507 | 5950996 | a | 0 | - | | chr18 | 9282709 | 9282961 | a | 0 | - | | chr19 | 536170 | 536504 | a | 0 | - | | chr22 | 6787794 | 6788999 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chrY | 7875294 | 7883380 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpfz74am9n/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chrY 7875294 7883380 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chrY | 7875294 | 7883380 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9250605 | 9260109 | a | 0 | + | | chr1 | 5323170 | 5330926 | a | 0 | + | | chr1 | 2477060 | 2486564 | a | 0 | + | | chr1 | 1456878 | 1466238 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr12 | 2377143 | 2386647 | a | 0 | + | | chr12 | 7084598 | 7094102 | a | 0 | - | | chr19 | 8244180 | 8253684 | a | 0 | + | | chr19 | 1 | 3229 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp8x9ogn0p/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2477060 2486564 a 0 + 1 1 chr1 5323170 5330926 a 0 + 2 2 chr1 9250605 9260109 a 0 + 3 3 chr1 1402835 1412339 a 0 - 4 4 chr1 1456878 1466238 a 0 - 5 5 chr12 2377143 2386647 a 0 + 6 6 chr12 7084598 7094102 a 0 - 7 7 chr19 1 3229 a 0 + 8 8 chr19 8244180 8253684 a 0 + 9 9 chr5 3730485 3734169 a 0 + 10 10 chr6 5699605 5708830 a 0 + 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9250605 | 9260109 | a | 0 | + | | chr1 | 5323170 | 5330926 | a | 0 | + | | chr1 | 2477060 | 2486564 | a | 0 | + | | chr1 | 1456878 | 1466238 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr12 | 2377143 | 2386647 | a | 0 | + | | chr12 | 7084598 | 7094102 | a | 0 | - | | chr19 | 8244180 | 8253684 | a | 0 | + | | chr19 | 1 | 3229 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 9436 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpqqotzs71/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 9436 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 9436 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4329446 | 4331255 | a | 0 | + | | chr1 | 3093760 | 3101405 | a | 0 | - | | chr11 | 7112207 | 7117224 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp18u4sf90/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 4329446 4331255 a 0 + 1 1 chr1 3093760 3101405 a 0 - 2 2 chr11 7112207 7117224 a 0 - 3 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4329446 | 4331255 | a | 0 | + | | chr1 | 3093760 | 3101405 | a | 0 | - | | chr11 | 7112207 | 7117224 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2394436 | 2395417 | a | 0 | + | | chr1 | 2394436 | 2401936 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp7byxp4ph/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2394436 2395417 a 0 + 1 1 chr1 2394436 2401936 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2394436 | 2395417 | a | 0 | + | | chr1 | 2394436 | 2401936 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9167123 | 9168045 | a | 0 | + | | chr1 | 6206766 | 6208601 | a | 0 | + | | chr1 | 6735287 | 6739856 | a | 0 | + | | chr1 | 2129422 | 2130695 | a | 0 | - | | chr10 | 6166446 | 6173000 | a | 0 | - | | chr10 | 1386730 | 1387969 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpqq8s4fhj/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 6206766 6208601 a 0 + 1 1 chr1 6735287 6739856 a 0 + 2 2 chr1 9167123 9168045 a 0 + 3 3 chr1 2129422 2130695 a 0 - 4 4 chr10 1386730 1387969 a 0 - 5 5 chr10 6166446 6173000 a 0 - 6 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9167123 | 9168045 | a | 0 | + | | chr1 | 6206766 | 6208601 | a | 0 | + | | chr1 | 6735287 | 6739856 | a | 0 | + | | chr1 | 2129422 | 2130695 | a | 0 | - | | chr10 | 6166446 | 6173000 | a | 0 | - | | chr10 | 1386730 | 1387969 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr2 | 9609193 | 9610699 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpv2vwc_pi/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr2 9609193 9610699 a 0 - 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr2 | 9609193 | 9610699 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3892213 | 3901862 | a | 0 | + | | chr1 | 365828 | 374901 | a | 0 | + | | chr1 | 3524731 | 3530881 | a | 0 | + | | chr1 | 2815051 | 2819179 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr12 | 8568789 | 8568790 | a | 0 | - | | chr17 | 2659454 | 2663582 | a | 0 | + | | chr18 | 5383053 | 5388648 | a | 0 | - | | chrM | 2517463 | 2526197 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 7 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpu3k6d0jg/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 365828 374901 a 0 + 1 1 chr1 3524731 3530881 a 0 + 2 2 chr1 3892213 3901862 a 0 + 3 3 chr1 561622 562809 a 0 - 4 4 chr1 2815051 2819179 a 0 - 5 5 chr12 8568789 8568790 a 0 - 6 6 chr17 2659454 2663582 a 0 + 7 7 chr18 5383053 5388648 a 0 - 8 8 chr5 8270775 8271518 a 0 - 9 9 chr8 6861070 6865767 a 0 + 10 10 chrM 2517463 2526197 a 0 + 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3892213 | 3901862 | a | 0 | + | | chr1 | 365828 | 374901 | a | 0 | + | | chr1 | 3524731 | 3530881 | a | 0 | + | | chr1 | 2815051 | 2819179 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr12 | 8568789 | 8568790 | a | 0 | - | | chr17 | 2659454 | 2663582 | a | 0 | + | | chr18 | 5383053 | 5388648 | a | 0 | - | | chrM | 2517463 | 2526197 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 7 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5131268 | 5132544 | a | 0 | + | | chr1 | 3029731 | 3035890 | a | 0 | - | | chr1 | 7912082 | 7913358 | a | 0 | - | | chr2 | 2664585 | 2671705 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr12 | 10000000 | 10006612 | a | 0 | + | | chr12 | 8536110 | 8538086 | a | 0 | + | | chr17 | 9999999 | 10000248 | a | 0 | + | | chr21 | 1506610 | 1514912 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 8 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp3qxs_u9t/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 5131268 5132544 a 0 + 1 1 chr1 3029731 3035890 a 0 - 2 2 chr1 7912082 7913358 a 0 - 3 3 chr10 6404400 6414399 a 0 - 4 4 chr11 6523872 6531293 a 0 + 5 5 chr12 8536110 8538086 a 0 + 6 6 chr12 10000000 10006612 a 0 + 7 7 chr17 9999999 10000248 a 0 + 8 8 chr2 2664585 2671705 a 0 - 9 9 chr21 1506610 1514912 a 0 + 10 10 chr4 3436636 3445507 a 0 + 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5131268 | 5132544 | a | 0 | + | | chr1 | 3029731 | 3035890 | a | 0 | - | | chr1 | 7912082 | 7913358 | a | 0 | - | | chr2 | 2664585 | 2671705 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr12 | 10000000 | 10006612 | a | 0 | + | | chr12 | 8536110 | 8538086 | a | 0 | + | | chr17 | 9999999 | 10000248 | a | 0 | + | | chr21 | 1506610 | 1514912 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 8 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 854199 | 862255 | a | 0 | + | | chr1 | 2678960 | 2685840 | a | 0 | + | | chr1 | 827476 | 829024 | a | 0 | + | | chr1 | 1597686 | 1604958 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr1 | 4600292 | 4608739 | a | 0 | + | | chr1 | 8285327 | 8288494 | a | 0 | + | | chr1 | 2379672 | 2388370 | a | 0 | - | | chr1 | 553963 | 555133 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpcyfmaky3/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 827476 829024 a 0 + 1 1 chr1 854199 862255 a 0 + 2 2 chr1 1597686 1604958 a 0 + 3 3 chr1 2678960 2685840 a 0 + 4 4 chr1 4600292 4608739 a 0 + 5 5 chr1 8285327 8288494 a 0 + 6 6 chr1 553963 555133 a 0 - 7 7 chr1 2379672 2388370 a 0 - 8 8 chr11 4803545 4805277 a 0 - 9 9 chr11 8196456 8199663 a 0 - 10 10 chr13 1361182 1371131 a 0 - 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 854199 | 862255 | a | 0 | + | | chr1 | 2678960 | 2685840 | a | 0 | + | | chr1 | 827476 | 829024 | a | 0 | + | | chr1 | 1597686 | 1604958 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr1 | 4600292 | 4608739 | a | 0 | + | | chr1 | 8285327 | 8288494 | a | 0 | + | | chr1 | 2379672 | 2388370 | a | 0 | - | | chr1 | 553963 | 555133 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6449547 | 6458308 | a | 0 | + | | chr1 | 9125819 | 9130795 | a | 0 | + | | chr1 | 6340267 | 6346553 | a | 0 | - | | chr1 | 3554720 | 3560186 | a | 0 | - | | chr1 | 1438042 | 1439067 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp73id6jpx/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 6449547 6458308 a 0 + 1 1 chr1 9125819 9130795 a 0 + 2 2 chr1 1438042 1439067 a 0 - 3 3 chr1 3554720 3560186 a 0 - 4 4 chr1 6340267 6346553 a 0 - 5 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6449547 | 6458308 | a | 0 | + | | chr1 | 9125819 | 9130795 | a | 0 | + | | chr1 | 6340267 | 6346553 | a | 0 | - | | chr1 | 3554720 | 3560186 | a | 0 | - | | chr1 | 1438042 | 1439067 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 3784 | a | 0 | + | | chr8 | 4153750 | 4161692 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpii76vw54/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 3784 a 0 + 1 1 chr8 4153750 4161692 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 3784 | a | 0 | + | | chr8 | 4153750 | 4161692 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3728240 | 3730813 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmphijnq7n6/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 3728240 3730813 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3728240 | 3730813 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8170813 | 8174915 | a | 0 | + | | chr1 | 7791503 | 7799993 | a | 0 | + | | chr1 | 5882446 | 5887377 | a | 0 | - | | chr1 | 8195355 | 8199260 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr11 | 8170813 | 8174391 | a | 0 | - | | chr13 | 529581 | 536403 | a | 0 | - | | chr13 | 8170813 | 8171716 | a | 0 | - | | chr20 | 8170813 | 8173225 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 7 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp0l2d7i90/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 7791503 7799993 a 0 + 1 1 chr1 8170813 8174915 a 0 + 2 2 chr1 5882446 5887377 a 0 - 3 3 chr1 8195355 8199260 a 0 - 4 4 chr11 8170813 8174391 a 0 - 5 5 chr13 529581 536403 a 0 - 6 6 chr13 8170813 8171716 a 0 - 7 7 chr20 8170813 8173225 a 0 - 8 8 chr4 10000000 10000733 a 0 - 9 9 chr6 8812996 8813324 a 0 - 10 10 chr9 8907436 8915615 a 0 - 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8170813 | 8174915 | a | 0 | + | | chr1 | 7791503 | 7799993 | a | 0 | + | | chr1 | 5882446 | 5887377 | a | 0 | - | | chr1 | 8195355 | 8199260 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr11 | 8170813 | 8174391 | a | 0 | - | | chr13 | 529581 | 536403 | a | 0 | - | | chr13 | 8170813 | 8171716 | a | 0 | - | | chr20 | 8170813 | 8173225 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 7 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 810 | a | 0 | - | | chr1 | 9210843 | 9214231 | a | 0 | - | | chrY | 3311371 | 3317532 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp1w3ieh4w/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 810 a 0 - 1 1 chr1 9210843 9214231 a 0 - 2 2 chrY 3311371 3317532 a 0 - 3 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 810 | a | 0 | - | | chr1 | 9210843 | 9214231 | a | 0 | - | | chrY | 3311371 | 3317532 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chrX | 5041143 | 5041870 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp4u5e50zi/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chrX 5041143 5041870 a 0 - 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chrX | 5041143 | 5041870 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7064027 | 7073278 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpw5z9mziu/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 7064027 7073278 a 0 - 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7064027 | 7073278 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1517917 | 1518405 | a | 0 | - | | chr2 | 4262688 | 4271760 | a | 0 | + | | chr5 | 1486260 | 1494176 | a | 0 | - | | chr7 | 887619 | 896023 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpmttcgw0i/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1517917 1518405 a 0 - 1 1 chr2 4262688 4271760 a 0 + 2 2 chr5 1486260 1494176 a 0 - 3 3 chr7 887619 896023 a 0 + 4 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1517917 | 1518405 | a | 0 | - | | chr2 | 4262688 | 4271760 | a | 0 | + | | chr5 | 1486260 | 1494176 | a | 0 | - | | chr7 | 887619 | 896023 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6153910 | 6159014 | a | 0 | + | | chr2 | 2636171 | 2636238 | a | 0 | + | | chr18 | 7463773 | 7463970 | a | 0 | + | | chr18 | 2446765 | 2451459 | a | 0 | + | | chr18 | 8236299 | 8243465 | a | 0 | - | | chr18 | 7408053 | 7410260 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpcwaakmqv/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 6153910 6159014 a 0 + 1 1 chr18 2446765 2451459 a 0 + 2 2 chr18 7463773 7463970 a 0 + 3 3 chr18 7408053 7410260 a 0 - 4 4 chr18 8236299 8243465 a 0 - 5 5 chr2 2636171 2636238 a 0 + 6 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6153910 | 6159014 | a | 0 | + | | chr2 | 2636171 | 2636238 | a | 0 | + | | chr18 | 7463773 | 7463970 | a | 0 | + | | chr18 | 2446765 | 2451459 | a | 0 | + | | chr18 | 8236299 | 8243465 | a | 0 | - | | chr18 | 7408053 | 7410260 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 830763 | 833436 | a | 0 | + | | chr1 | 5529007 | 5529063 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpgjavy4ms/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 830763 833436 a 0 + 1 1 chr1 5529007 5529063 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 830763 | 833436 | a | 0 | + | | chr1 | 5529007 | 5529063 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2371118 | 2373698 | a | 0 | + | | chr1 | 2371118 | 2371119 | a | 0 | - | | chr1 | 2371118 | 2374234 | a | 0 | - | | chr1 | 2371118 | 2371467 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpw7ses0d0/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2371118 2373698 a 0 + 1 1 chr1 2371118 2371119 a 0 - 2 2 chr1 2371118 2371467 a 0 - 2 3 chr1 2371118 2374234 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2371118 | 2373698 | a | 0 | + | | chr1 | 2371118 | 2371119 | a | 0 | - | | chr1 | 2371118 | 2374234 | a | 0 | - | | chr1 | 2371118 | 2371467 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9073604 | 9082802 | a | 0 | + | | chr1 | 257002 | 258574 | a | 0 | + | | chr1 | 8196080 | 8197652 | a | 0 | - | | chr1 | 8697310 | 8699378 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr9 | 7423657 | 7426687 | a | 0 | - | | chr11 | 6559438 | 6567490 | a | 0 | - | | chr22 | 4313509 | 4315142 | a | 0 | - | | chrY | 4423250 | 4431855 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpqj0977l6/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 257002 258574 a 0 + 1 1 chr1 9073604 9082802 a 0 + 2 2 chr1 7184725 7192783 a 0 - 3 3 chr1 7337106 7345570 a 0 - 4 4 chr1 8196080 8197652 a 0 - 5 5 chr1 8697310 8699378 a 0 - 6 6 chr11 6559438 6567490 a 0 - 7 7 chr22 4313509 4315142 a 0 - 8 8 chr8 9210192 9214707 a 0 - 9 9 chr9 7423657 7426687 a 0 - 10 10 chrY 4423250 4431855 a 0 - 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9073604 | 9082802 | a | 0 | + | | chr1 | 257002 | 258574 | a | 0 | + | | chr1 | 8196080 | 8197652 | a | 0 | - | | chr1 | 8697310 | 8699378 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr9 | 7423657 | 7426687 | a | 0 | - | | chr11 | 6559438 | 6567490 | a | 0 | - | | chr22 | 4313509 | 4315142 | a | 0 | - | | chrY | 4423250 | 4431855 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 6496 | a | 0 | + | | chr1 | 5519453 | 5522955 | a | 0 | + | | chr1 | 2746016 | 2748213 | a | 0 | + | | chr1 | 8779896 | 8780820 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr15 | 3887503 | 3889723 | a | 0 | + | | chr17 | 9334626 | 9338718 | a | 0 | + | | chr18 | 6256675 | 6259162 | a | 0 | + | | chr22 | 7231385 | 7231655 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 7 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpwca243e4/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 6496 a 0 + 1 1 chr1 2746016 2748213 a 0 + 2 2 chr1 5519453 5522955 a 0 + 3 3 chr1 6304097 6314090 a 0 + 4 4 chr1 8779896 8780820 a 0 + 5 5 chr14 2 9316 a 0 + 6 6 chr15 3887503 3889723 a 0 + 7 7 chr17 9334626 9338718 a 0 + 8 8 chr18 6256675 6259162 a 0 + 9 9 chr22 7231385 7231655 a 0 - 10 10 chr9 2385836 2390229 a 0 + 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 6496 | a | 0 | + | | chr1 | 5519453 | 5522955 | a | 0 | + | | chr1 | 2746016 | 2748213 | a | 0 | + | | chr1 | 8779896 | 8780820 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr15 | 3887503 | 3889723 | a | 0 | + | | chr17 | 9334626 | 9338718 | a | 0 | + | | chr18 | 6256675 | 6259162 | a | 0 | + | | chr22 | 7231385 | 7231655 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 7 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2791001 | 2798497 | a | 0 | - | | chr1 | 3840572 | 3840573 | a | 0 | - | | chr1 | 9324955 | 9326171 | a | 0 | - | | chr1 | 4276168 | 4278643 | a | 0 | - | | chr2 | 8859347 | 8859348 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpj56c12kk/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2791001 2798497 a 0 - 1 1 chr1 3840572 3840573 a 0 - 2 2 chr1 4276168 4278643 a 0 - 3 3 chr1 9324955 9326171 a 0 - 4 4 chr2 8859347 8859348 a 0 + 5 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2791001 | 2798497 | a | 0 | - | | chr1 | 3840572 | 3840573 | a | 0 | - | | chr1 | 9324955 | 9326171 | a | 0 | - | | chr1 | 4276168 | 4278643 | a | 0 | - | | chr2 | 8859347 | 8859348 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr2 | 829532 | 830726 | a | 0 | + | | chr2 | 4705482 | 4710776 | a | 0 | + | | chr2 | 829532 | 835469 | a | 0 | - | | chr2 | 5679390 | 5682047 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp42_y27ae/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr2 829532 830726 a 0 + 1 1 chr2 4705482 4710776 a 0 + 2 2 chr2 829532 835469 a 0 - 3 3 chr2 5679390 5682047 a 0 - 4 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr2 | 829532 | 830726 | a | 0 | + | | chr2 | 4705482 | 4710776 | a | 0 | + | | chr2 | 829532 | 835469 | a | 0 | - | | chr2 | 5679390 | 5682047 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6362159 | 6364896 | a | 0 | - | | chr3 | 6362159 | 6368885 | a | 0 | + | | chr5 | 6362159 | 6366691 | a | 0 | + | | chr8 | 6362159 | 6365685 | a | 0 | + | | chr11 | 6362159 | 6370839 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp24a8ae5e/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 6362159 6364896 a 0 - 1 1 chr11 6362159 6370839 a 0 + 2 2 chr3 6362159 6368885 a 0 + 3 3 chr5 6362159 6366691 a 0 + 4 4 chr8 6362159 6365685 a 0 + 5 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6362159 | 6364896 | a | 0 | - | | chr3 | 6362159 | 6368885 | a | 0 | + | | chr5 | 6362159 | 6366691 | a | 0 | + | | chr8 | 6362159 | 6365685 | a | 0 | + | | chr11 | 6362159 | 6370839 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2263457 | 2272558 | a | 0 | + | | chr1 | 2159654 | 2168755 | a | 0 | + | | chr1 | 1 | 7336 | a | 0 | + | | chr1 | 6626909 | 6626911 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr13 | 7395311 | 7404412 | a | 0 | + | | chr15 | 2965200 | 2974301 | a | 0 | - | | chr20 | 9821939 | 9831040 | a | 0 | + | | chr22 | 10000000 | 10009101 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpf2eepihz/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 7336 a 0 + 1 1 chr1 2159654 2168755 a 0 + 2 2 chr1 2263457 2272558 a 0 + 3 3 chr1 6626909 6626911 a 0 + 4 4 chr1 1 9102 a 0 - 5 5 chr1 2159654 2162918 a 0 - 6 6 chr1 10000000 10009101 a 0 - 7 7 chr13 7395311 7404412 a 0 + 8 8 chr15 2965200 2974301 a 0 - 9 9 chr20 9821939 9831040 a 0 + 10 10 chr22 10000000 10009101 a 0 - 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2263457 | 2272558 | a | 0 | + | | chr1 | 2159654 | 2168755 | a | 0 | + | | chr1 | 1 | 7336 | a | 0 | + | | chr1 | 6626909 | 6626911 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr13 | 7395311 | 7404412 | a | 0 | + | | chr15 | 2965200 | 2974301 | a | 0 | - | | chr20 | 9821939 | 9831040 | a | 0 | + | | chr22 | 10000000 | 10009101 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7126308 | 7128983 | a | 0 | + | | chr1 | 4134229 | 4140230 | a | 0 | - | | chr1 | 9547490 | 9557471 | a | 0 | - | | chr1 | 7126308 | 7129601 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr6 | 2731566 | 2736806 | a | 0 | - | | chr7 | 7126308 | 7128197 | a | 0 | + | | chr17 | 9083576 | 9093576 | a | 0 | + | | chrM | 5432328 | 5433212 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp5n08fsx4/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 7126308 7128983 a 0 + 1 1 chr1 4134229 4140230 a 0 - 2 2 chr1 6887505 6887863 a 0 - 3 3 chr1 7126308 7129601 a 0 - 4 4 chr1 9547490 9557471 a 0 - 5 5 chr17 9083576 9093576 a 0 + 6 6 chr5 3938692 3942702 a 0 + 7 7 chr5 4363471 4363858 a 0 + 8 8 chr6 2731566 2736806 a 0 - 9 9 chr7 7126308 7128197 a 0 + 10 10 chrM 5432328 5433212 a 0 + 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7126308 | 7128983 | a | 0 | + | | chr1 | 4134229 | 4140230 | a | 0 | - | | chr1 | 9547490 | 9557471 | a | 0 | - | | chr1 | 7126308 | 7129601 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr6 | 2731566 | 2736806 | a | 0 | - | | chr7 | 7126308 | 7128197 | a | 0 | + | | chr17 | 9083576 | 9093576 | a | 0 | + | | chrM | 5432328 | 5433212 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 521653 | 527229 | a | 0 | - | | chr1 | 664457 | 665273 | a | 0 | - | | chr21 | 4387153 | 4389374 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpig49ar94/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 521653 527229 a 0 - 1 1 chr1 664457 665273 a 0 - 2 2 chr21 4387153 4389374 a 0 - 3 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 521653 | 527229 | a | 0 | - | | chr1 | 664457 | 665273 | a | 0 | - | | chr21 | 4387153 | 4389374 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6833744 | 6840220 | a | 0 | + | | chr1 | 3168139 | 3174871 | a | 0 | + | | chr1 | 5138480 | 5148281 | a | 0 | + | | chr1 | 5969554 | 5976186 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr4 | 3168139 | 3172525 | a | 0 | - | | chr21 | 5866644 | 5868307 | a | 0 | + | | chrM | 2 | 6054 | a | 0 | + | | chrX | 8112474 | 8121581 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpggx_xgqo/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 3168139 3174871 a 0 + 1 1 chr1 5138480 5148281 a 0 + 2 2 chr1 5969554 5976186 a 0 + 3 3 chr1 6833744 6840220 a 0 + 4 4 chr1 1 5159 a 0 - 5 5 chr1 530949 530989 a 0 - 6 6 chr1 9845853 9849117 a 0 - 7 7 chr21 5866644 5868307 a 0 + 8 8 chr4 3168139 3172525 a 0 - 9 9 chrM 2 6054 a 0 + 10 10 chrX 8112474 8121581 a 0 + 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6833744 | 6840220 | a | 0 | + | | chr1 | 3168139 | 3174871 | a | 0 | + | | chr1 | 5138480 | 5148281 | a | 0 | + | | chr1 | 5969554 | 5976186 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr4 | 3168139 | 3172525 | a | 0 | - | | chr21 | 5866644 | 5868307 | a | 0 | + | | chrM | 2 | 6054 | a | 0 | + | | chrX | 8112474 | 8121581 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6409567 | 6409950 | a | 0 | + | | chr1 | 978411 | 981227 | a | 0 | - | | chr1 | 7974264 | 7978609 | a | 0 | - | | chr1 | 2487153 | 2492297 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr7 | 17652 | 20849 | a | 0 | + | | chr9 | 2487153 | 2489905 | a | 0 | + | | chr14 | 6098654 | 6103457 | a | 0 | + | | chr18 | 9928730 | 9929095 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpjvsrzqey/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 6409567 6409950 a 0 + 1 1 chr1 613908 620429 a 0 - 2 2 chr1 978411 981227 a 0 - 3 3 chr1 2487153 2492297 a 0 - 4 4 chr1 7974264 7978609 a 0 - 5 5 chr1 8490959 8493247 a 0 - 6 6 chr14 6098654 6103457 a 0 + 7 7 chr18 9928730 9929095 a 0 - 8 8 chr2 2487153 2494028 a 0 + 9 9 chr7 17652 20849 a 0 + 10 10 chr9 2487153 2489905 a 0 + 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6409567 | 6409950 | a | 0 | + | | chr1 | 978411 | 981227 | a | 0 | - | | chr1 | 7974264 | 7978609 | a | 0 | - | | chr1 | 2487153 | 2492297 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr7 | 17652 | 20849 | a | 0 | + | | chr9 | 2487153 | 2489905 | a | 0 | + | | chr14 | 6098654 | 6103457 | a | 0 | + | | chr18 | 9928730 | 9929095 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4168665 | 4170674 | a | 0 | - | | chr1 | 6931445 | 6935987 | a | 0 | - | | chr1 | 6874335 | 6880931 | a | 0 | - | | chr14 | 4463835 | 4469338 | a | 0 | - | | chr14 | 6893717 | 6900674 | a | 0 | - | | chr19 | 4109343 | 4112592 | a | 0 | + | | chrY | 1741915 | 1750209 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 7 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpy17d51e0/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 4168665 4170674 a 0 - 1 1 chr1 6874335 6880931 a 0 - 2 2 chr1 6931445 6935987 a 0 - 3 3 chr14 4463835 4469338 a 0 - 4 4 chr14 6893717 6900674 a 0 - 5 5 chr19 4109343 4112592 a 0 + 6 6 chrY 1741915 1750209 a 0 + 7 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4168665 | 4170674 | a | 0 | - | | chr1 | 6931445 | 6935987 | a | 0 | - | | chr1 | 6874335 | 6880931 | a | 0 | - | | chr14 | 4463835 | 4469338 | a | 0 | - | | chr14 | 6893717 | 6900674 | a | 0 | - | | chr19 | 4109343 | 4112592 | a | 0 | + | | chrY | 1741915 | 1750209 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 7 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1166897 | 1176249 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpcoiq9cq9/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1166897 1176249 a 0 - 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1166897 | 1176249 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 985685 | 993007 | a | 0 | + | | chr1 | 1073325 | 1080647 | a | 0 | + | | chr1 | 9761454 | 9768776 | a | 0 | + | | chr1 | 6402693 | 6410015 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr5 | 1073325 | 1080953 | a | 0 | - | | chr8 | 1073325 | 1080647 | a | 0 | + | | chr9 | 1073325 | 1080647 | a | 0 | - | | chr21 | 1073325 | 1080647 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpn1rpkbdp/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 985685 993007 a 0 + 1 1 chr1 1073325 1080647 a 0 + 2 2 chr1 6402693 6410015 a 0 + 3 3 chr1 9761454 9768776 a 0 + 4 4 chr1 1073325 1080647 a 0 - 5 5 chr1 1073325 1080647 a 0 - 5 6 chr1 8945459 8952781 a 0 - 6 7 chr21 1073325 1080647 a 0 + 7 8 chr5 1073325 1080953 a 0 - 8 9 chr8 1073325 1080647 a 0 + 9 10 chr9 1073325 1080647 a 0 - 10 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 985685 | 993007 | a | 0 | + | | chr1 | 1073325 | 1080647 | a | 0 | + | | chr1 | 9761454 | 9768776 | a | 0 | + | | chr1 | 6402693 | 6410015 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr5 | 1073325 | 1080953 | a | 0 | - | | chr8 | 1073325 | 1080647 | a | 0 | + | | chr9 | 1073325 | 1080647 | a | 0 | - | | chr21 | 1073325 | 1080647 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr14 | 2501967 | 2508274 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp3dlwhu7j/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr14 2501967 2508274 a 0 - 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr14 | 2501967 | 2508274 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6391739 | 6401345 | a | 0 | + | | chr1 | 6812847 | 6819912 | a | 0 | + | | chr1 | 6391739 | 6397940 | a | 0 | + | | chr1 | 10000000 | 10006456 | a | 0 | - | | chr1 | 7814039 | 7816533 | a | 0 | - | | chr12 | 6391739 | 6391740 | a | 0 | + | | chrM | 3665729 | 3675729 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 7 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp_r0uemq5/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 6391739 6397940 a 0 + 1 1 chr1 6391739 6401345 a 0 + 1 2 chr1 6812847 6819912 a 0 + 2 3 chr1 7814039 7816533 a 0 - 3 4 chr1 10000000 10006456 a 0 - 4 5 chr12 6391739 6391740 a 0 + 5 6 chrM 3665729 3675729 a 0 - 6 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6391739 | 6401345 | a | 0 | + | | chr1 | 6812847 | 6819912 | a | 0 | + | | chr1 | 6391739 | 6397940 | a | 0 | + | | chr1 | 10000000 | 10006456 | a | 0 | - | | chr1 | 7814039 | 7816533 | a | 0 | - | | chr12 | 6391739 | 6391740 | a | 0 | + | | chrM | 3665729 | 3675729 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 7 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5775791 | 5780166 | a | 0 | - | | chr1 | 6908195 | 6914094 | a | 0 | - | | chr4 | 4489539 | 4499539 | a | 0 | + | | chr17 | 5819577 | 5827172 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp38jxz5yh/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 5775791 5780166 a 0 - 1 1 chr1 6908195 6914094 a 0 - 2 2 chr17 5819577 5827172 a 0 - 3 3 chr4 4489539 4499539 a 0 + 4 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5775791 | 5780166 | a | 0 | - | | chr1 | 6908195 | 6914094 | a | 0 | - | | chr4 | 4489539 | 4499539 | a | 0 | + | | chr17 | 5819577 | 5827172 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7558948 | 7567138 | a | 0 | + | | chr1 | 9944999 | 9945604 | a | 0 | - | | chr6 | 7558948 | 7564626 | a | 0 | - | | chr11 | 3124314 | 3126074 | a | 0 | - | | chr13 | 8290190 | 8297976 | a | 0 | - | | chr15 | 6579110 | 6580870 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpgu5f2qvh/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 7558948 7567138 a 0 + 1 1 chr1 9944999 9945604 a 0 - 2 2 chr11 3124314 3126074 a 0 - 3 3 chr13 8290190 8297976 a 0 - 4 4 chr15 6579110 6580870 a 0 + 5 5 chr6 7558948 7564626 a 0 - 6 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7558948 | 7567138 | a | 0 | + | | chr1 | 9944999 | 9945604 | a | 0 | - | | chr6 | 7558948 | 7564626 | a | 0 | - | | chr11 | 3124314 | 3126074 | a | 0 | - | | chr13 | 8290190 | 8297976 | a | 0 | - | | chr15 | 6579110 | 6580870 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3906212 | 3914061 | a | 0 | + | | chr1 | 8685753 | 8695387 | a | 0 | + | | chr1 | 8685753 | 8695660 | a | 0 | - | | chr1 | 6162664 | 6164194 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr14 | 8685753 | 8695301 | a | 0 | - | | chr20 | 8442069 | 8447444 | a | 0 | + | | chr22 | 6274262 | 6278494 | a | 0 | - | | chrM | 8685753 | 8687713 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 8 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp2civa_0b/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 3906212 3914061 a 0 + 1 1 chr1 8685753 8695387 a 0 + 2 2 chr1 6162664 6164194 a 0 - 3 3 chr1 8685753 8695660 a 0 - 4 4 chr11 8685753 8691808 a 0 + 5 5 chr13 909122 912715 a 0 - 6 6 chr14 8685753 8695301 a 0 - 7 7 chr2 1859834 1859835 a 0 + 8 8 chr20 8442069 8447444 a 0 + 9 9 chr22 6274262 6278494 a 0 - 10 10 chrM 8685753 8687713 a 0 - 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3906212 | 3914061 | a | 0 | + | | chr1 | 8685753 | 8695387 | a | 0 | + | | chr1 | 8685753 | 8695660 | a | 0 | - | | chr1 | 6162664 | 6164194 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr14 | 8685753 | 8695301 | a | 0 | - | | chr20 | 8442069 | 8447444 | a | 0 | + | | chr22 | 6274262 | 6278494 | a | 0 | - | | chrM | 8685753 | 8687713 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 8 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 886194 | 886404 | a | 0 | + | | chr1 | 6579483 | 6585025 | a | 0 | + | | chr16 | 641637 | 647673 | a | 0 | + | | chrX | 2298917 | 2303127 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpj44jbtbk/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 886194 886404 a 0 + 1 1 chr1 6579483 6585025 a 0 + 2 2 chr16 641637 647673 a 0 + 3 3 chrX 2298917 2303127 a 0 + 4 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 886194 | 886404 | a | 0 | + | | chr1 | 6579483 | 6585025 | a | 0 | + | | chr16 | 641637 | 647673 | a | 0 | + | | chrX | 2298917 | 2303127 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6364260 | 6372302 | a | 0 | + | | chr1 | 10000000 | 10009602 | a | 0 | + | | chr1 | 9714138 | 9722312 | a | 0 | + | | chr1 | 2215071 | 2217290 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr12 | 9699814 | 9703903 | a | 0 | + | | chr13 | 10000000 | 10008042 | a | 0 | - | | chr17 | 4916587 | 4924629 | a | 0 | + | | chr18 | 4024579 | 4025932 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 8 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp4_kbqlja/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2215071 2217290 a 0 + 1 1 chr1 6364260 6372302 a 0 + 2 2 chr1 9714138 9722312 a 0 + 3 3 chr1 10000000 10009602 a 0 + 4 4 chr12 9699814 9703903 a 0 + 5 5 chr13 10000000 10008042 a 0 - 6 6 chr17 4916587 4924629 a 0 + 7 7 chr18 4024579 4025932 a 0 + 8 8 chr5 4854325 4862367 a 0 + 9 9 chr7 1697804 1703233 a 0 + 10 10 chr9 2613526 2621305 a 0 - 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6364260 | 6372302 | a | 0 | + | | chr1 | 10000000 | 10009602 | a | 0 | + | | chr1 | 9714138 | 9722312 | a | 0 | + | | chr1 | 2215071 | 2217290 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr12 | 9699814 | 9703903 | a | 0 | + | | chr13 | 10000000 | 10008042 | a | 0 | - | | chr17 | 4916587 | 4924629 | a | 0 | + | | chr18 | 4024579 | 4025932 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 8 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr2 | 1 | 7095 | a | 0 | - | | chrX | 7284259 | 7284772 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpdqkhu_xk/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr2 1 7095 a 0 - 1 1 chrX 7284259 7284772 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr2 | 1 | 7095 | a | 0 | - | | chrX | 7284259 | 7284772 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5852544 | 5862494 | a | 0 | + | | chr1 | 5852544 | 5862494 | a | 0 | - | | chr11 | 5852544 | 5862494 | a | 0 | - | | chrM | 5852544 | 5862494 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpm_hcsyy7/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 5852544 5862494 a 0 + 1 1 chr1 5852544 5862494 a 0 - 2 2 chr11 5852544 5862494 a 0 - 3 3 chrM 5852544 5862494 a 0 + 4 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5852544 | 5862494 | a | 0 | + | | chr1 | 5852544 | 5862494 | a | 0 | - | | chr11 | 5852544 | 5862494 | a | 0 | - | | chrM | 5852544 | 5862494 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2074450 | 2081859 | a | 0 | - | | chr6 | 7842583 | 7849112 | a | 0 | + | | chr9 | 7564466 | 7565507 | a | 0 | + | | chr12 | 3296360 | 3298816 | a | 0 | + | | chr15 | 975384 | 983089 | a | 0 | - | | chr15 | 7906920 | 7908961 | a | 0 | - | | chr16 | 1439443 | 1443673 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 7 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpyxnjysm2/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2074450 2081859 a 0 - 1 1 chr12 3296360 3298816 a 0 + 2 2 chr15 975384 983089 a 0 - 3 3 chr15 7906920 7908961 a 0 - 4 4 chr16 1439443 1443673 a 0 - 5 5 chr6 7842583 7849112 a 0 + 6 6 chr9 7564466 7565507 a 0 + 7 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2074450 | 2081859 | a | 0 | - | | chr6 | 7842583 | 7849112 | a | 0 | + | | chr9 | 7564466 | 7565507 | a | 0 | + | | chr12 | 3296360 | 3298816 | a | 0 | + | | chr15 | 975384 | 983089 | a | 0 | - | | chr15 | 7906920 | 7908961 | a | 0 | - | | chr16 | 1439443 | 1443673 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 7 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8632550 | 8639790 | a | 0 | + | | chr1 | 7856254 | 7859970 | a | 0 | + | | chr1 | 7856254 | 7863494 | a | 0 | - | | chr1 | 4157676 | 4158765 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr1 | 5271424 | 5280809 | a | 0 | - | | chr1 | 1809297 | 1816537 | a | 0 | - | | chr1 | 7962285 | 7969525 | a | 0 | - | | chr1 | 9634680 | 9638908 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpsovkb3o1/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 7856254 7859970 a 0 + 1 1 chr1 8632550 8639790 a 0 + 2 2 chr1 1809297 1816537 a 0 - 3 3 chr1 4157676 4158765 a 0 - 4 4 chr1 5271424 5280809 a 0 - 5 5 chr1 7856254 7863494 a 0 - 6 6 chr1 7962285 7969525 a 0 - 7 7 chr1 9634680 9638908 a 0 - 8 8 chr13 2844908 2845838 a 0 + 9 9 chr4 7856254 7859334 a 0 - 10 10 chr9 2245330 2252570 a 0 + 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8632550 | 8639790 | a | 0 | + | | chr1 | 7856254 | 7859970 | a | 0 | + | | chr1 | 7856254 | 7863494 | a | 0 | - | | chr1 | 4157676 | 4158765 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr1 | 5271424 | 5280809 | a | 0 | - | | chr1 | 1809297 | 1816537 | a | 0 | - | | chr1 | 7962285 | 7969525 | a | 0 | - | | chr1 | 9634680 | 9638908 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 747107 | 756054 | a | 0 | + | | chr1 | 6052553 | 6055411 | a | 0 | + | | chr11 | 9157034 | 9159532 | a | 0 | - | | chr20 | 1318160 | 1325395 | a | 0 | + | | chrM | 3851410 | 3854050 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp9viaf9qi/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 747107 756054 a 0 + 1 1 chr1 6052553 6055411 a 0 + 2 2 chr11 9157034 9159532 a 0 - 3 3 chr20 1318160 1325395 a 0 + 4 4 chrM 3851410 3854050 a 0 - 5 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 747107 | 756054 | a | 0 | + | | chr1 | 6052553 | 6055411 | a | 0 | + | | chr11 | 9157034 | 9159532 | a | 0 | - | | chr20 | 1318160 | 1325395 | a | 0 | + | | chrM | 3851410 | 3854050 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3250898 | 3252542 | a | 0 | + | | chr1 | 1218094 | 1225739 | a | 0 | + | | chr1 | 1218094 | 1222825 | a | 0 | + | | chr2 | 4627002 | 4627290 | a | 0 | - | | chr17 | 3698909 | 3699531 | a | 0 | + | | chr18 | 3920841 | 3921229 | a | 0 | + | | chr18 | 9400064 | 9400452 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 7 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpjc83sp0g/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1218094 1222825 a 0 + 1 1 chr1 1218094 1225739 a 0 + 1 2 chr1 3250898 3252542 a 0 + 2 3 chr17 3698909 3699531 a 0 + 3 4 chr18 3920841 3921229 a 0 + 4 5 chr18 9400064 9400452 a 0 - 5 6 chr2 4627002 4627290 a 0 - 6 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3250898 | 3252542 | a | 0 | + | | chr1 | 1218094 | 1225739 | a | 0 | + | | chr1 | 1218094 | 1222825 | a | 0 | + | | chr2 | 4627002 | 4627290 | a | 0 | - | | chr17 | 3698909 | 3699531 | a | 0 | + | | chr18 | 3920841 | 3921229 | a | 0 | + | | chr18 | 9400064 | 9400452 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 7 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2071537 | 2073512 | a | 0 | + | | chr4 | 841406 | 842428 | a | 0 | + | | chr8 | 2896305 | 2900223 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp2bu10kt9/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2071537 2073512 a 0 + 1 1 chr4 841406 842428 a 0 + 2 2 chr8 2896305 2900223 a 0 + 3 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2071537 | 2073512 | a | 0 | + | | chr4 | 841406 | 842428 | a | 0 | + | | chr8 | 2896305 | 2900223 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr17 | 8227556 | 8232060 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpv5r47vr9/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr17 8227556 8232060 a 0 - 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr17 | 8227556 | 8232060 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr13 | 5781394 | 5784338 | a | 0 | - | | chr21 | 5781394 | 5787491 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp4xeveh20/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr13 5781394 5784338 a 0 - 1 1 chr21 5781394 5787491 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr13 | 5781394 | 5784338 | a | 0 | - | | chr21 | 5781394 | 5787491 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4066213 | 4070004 | a | 0 | + | | chr1 | 7573283 | 7576284 | a | 0 | - | | chr6 | 2105576 | 2108366 | a | 0 | - | | chr8 | 1763478 | 1769481 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpuwnx9cgx/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 4066213 4070004 a 0 + 1 1 chr1 7573283 7576284 a 0 - 2 2 chr6 2105576 2108366 a 0 - 3 3 chr8 1763478 1769481 a 0 - 4 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4066213 | 4070004 | a | 0 | + | | chr1 | 7573283 | 7576284 | a | 0 | - | | chr6 | 2105576 | 2108366 | a | 0 | - | | chr8 | 1763478 | 1769481 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2442270 | 2449078 | a | 0 | + | | chr1 | 7643131 | 7649703 | a | 0 | + | | chr1 | 863086 | 872478 | a | 0 | + | | chr1 | 8080305 | 8085469 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr10 | 9470355 | 9475069 | a | 0 | + | | chr19 | 7513190 | 7518002 | a | 0 | + | | chr20 | 2673017 | 2675909 | a | 0 | - | | chr22 | 4743240 | 4749252 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmprkft3x7f/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 863086 872478 a 0 + 1 1 chr1 2442270 2449078 a 0 + 2 2 chr1 7643131 7649703 a 0 + 3 3 chr1 2 6785 a 0 - 4 4 chr1 5173309 5181402 a 0 - 5 5 chr1 8080305 8085469 a 0 - 6 6 chr10 9470355 9475069 a 0 + 7 7 chr19 7513190 7518002 a 0 + 8 8 chr20 2673017 2675909 a 0 - 9 9 chr22 4743240 4749252 a 0 + 10 10 chr4 2957601 2961754 a 0 - 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2442270 | 2449078 | a | 0 | + | | chr1 | 7643131 | 7649703 | a | 0 | + | | chr1 | 863086 | 872478 | a | 0 | + | | chr1 | 8080305 | 8085469 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr10 | 9470355 | 9475069 | a | 0 | + | | chr19 | 7513190 | 7518002 | a | 0 | + | | chr20 | 2673017 | 2675909 | a | 0 | - | | chr22 | 4743240 | 4749252 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr11 | 1487476 | 1489156 | a | 0 | + | | chr11 | 3871339 | 3872183 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp_ldmmdmd/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr11 1487476 1489156 a 0 + 1 1 chr11 3871339 3872183 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr11 | 1487476 | 1489156 | a | 0 | + | | chr11 | 3871339 | 3872183 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7942155 | 7944940 | a | 0 | + | | chr1 | 8050289 | 8051031 | a | 0 | + | | chr1 | 2253072 | 2262297 | a | 0 | - | | chr1 | 1218239 | 1227297 | a | 0 | - | | chr13 | 1765266 | 1766600 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpmrpowutc/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 7942155 7944940 a 0 + 1 1 chr1 8050289 8051031 a 0 + 2 2 chr1 1218239 1227297 a 0 - 3 3 chr1 2253072 2262297 a 0 - 4 4 chr13 1765266 1766600 a 0 - 5 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7942155 | 7944940 | a | 0 | + | | chr1 | 8050289 | 8051031 | a | 0 | + | | chr1 | 2253072 | 2262297 | a | 0 | - | | chr1 | 1218239 | 1227297 | a | 0 | - | | chr13 | 1765266 | 1766600 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1279781 | 1285735 | a | 0 | + | | chr1 | 1279781 | 1281720 | a | 0 | - | | chr18 | 1539947 | 1549426 | a | 0 | - | | chr19 | 216454 | 216496 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpmckmqbo3/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1279781 1285735 a 0 + 1 1 chr1 1279781 1281720 a 0 - 2 2 chr18 1539947 1549426 a 0 - 3 3 chr19 216454 216496 a 0 + 4 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1279781 | 1285735 | a | 0 | + | | chr1 | 1279781 | 1281720 | a | 0 | - | | chr18 | 1539947 | 1549426 | a | 0 | - | | chr19 | 216454 | 216496 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8832927 | 8842165 | a | 0 | + | | chr1 | 4300182 | 4307628 | a | 0 | + | | chr1 | 3810358 | 3812119 | a | 0 | + | | chr1 | 8741447 | 8746581 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr3 | 6070653 | 6080653 | a | 0 | - | | chr6 | 3152607 | 3153468 | a | 0 | - | | chr14 | 4934844 | 4937623 | a | 0 | - | | chr18 | 2267020 | 2276316 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 10 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpmd2jpkig/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 3810358 3812119 a 0 + 1 1 chr1 4300182 4307628 a 0 + 2 2 chr1 8669840 8673086 a 0 + 3 3 chr1 8741447 8746581 a 0 + 4 4 chr1 8832927 8842165 a 0 + 5 5 chr1 5560049 5562256 a 0 - 6 6 chr14 4934844 4937623 a 0 - 7 7 chr18 2267020 2276316 a 0 + 8 8 chr3 6070653 6080653 a 0 - 9 9 chr6 3152607 3153468 a 0 - 10 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8832927 | 8842165 | a | 0 | + | | chr1 | 4300182 | 4307628 | a | 0 | + | | chr1 | 3810358 | 3812119 | a | 0 | + | | chr1 | 8741447 | 8746581 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr3 | 6070653 | 6080653 | a | 0 | - | | chr6 | 3152607 | 3153468 | a | 0 | - | | chr14 | 4934844 | 4937623 | a | 0 | - | | chr18 | 2267020 | 2276316 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 10 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2711611 | 2718931 | a | 0 | + | | chr1 | 3109457 | 3109901 | a | 0 | - | | chr1 | 4936221 | 4936962 | a | 0 | - | | chr1 | 1054956 | 1060548 | a | 0 | - | | chr1 | 4138964 | 4148014 | a | 0 | - | | chr1 | 4393214 | 4393955 | a | 0 | - | | chr20 | 475391 | 478893 | a | 0 | - | | chr21 | 2420969 | 2427761 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 8 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpdj4othm5/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2711611 2718931 a 0 + 1 1 chr1 1054956 1060548 a 0 - 2 2 chr1 3109457 3109901 a 0 - 3 3 chr1 4138964 4148014 a 0 - 4 4 chr1 4393214 4393955 a 0 - 5 5 chr1 4936221 4936962 a 0 - 6 6 chr20 475391 478893 a 0 - 7 7 chr21 2420969 2427761 a 0 - 8 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2711611 | 2718931 | a | 0 | + | | chr1 | 3109457 | 3109901 | a | 0 | - | | chr1 | 4936221 | 4936962 | a | 0 | - | | chr1 | 1054956 | 1060548 | a | 0 | - | | chr1 | 4138964 | 4148014 | a | 0 | - | | chr1 | 4393214 | 4393955 | a | 0 | - | | chr20 | 475391 | 478893 | a | 0 | - | | chr21 | 2420969 | 2427761 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 8 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7681235 | 7687648 | a | 0 | + | | chr4 | 6643738 | 6644052 | a | 0 | - | | chr22 | 9129968 | 9131097 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpcjo19q92/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 7681235 7687648 a 0 + 1 1 chr22 9129968 9131097 a 0 - 2 2 chr4 6643738 6644052 a 0 - 3 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7681235 | 7687648 | a | 0 | + | | chr4 | 6643738 | 6644052 | a | 0 | - | | chr22 | 9129968 | 9131097 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8213480 | 8219173 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp4svo8mrl/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 8213480 8219173 a 0 - 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8213480 | 8219173 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9180771 | 9187484 | a | 0 | + | | chr1 | 7067807 | 7074520 | a | 0 | + | | chr1 | 1 | 6714 | a | 0 | + | | chr1 | 4452539 | 4456203 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr6 | 1920717 | 1927430 | a | 0 | + | | chr9 | 5275053 | 5281766 | a | 0 | + | | chr14 | 7810301 | 7817014 | a | 0 | + | | chr22 | 8988597 | 8995310 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp_6_xx2_9/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 6714 a 0 + 1 1 chr1 4452539 4456203 a 0 + 2 2 chr1 7067807 7074520 a 0 + 3 3 chr1 9180771 9187484 a 0 + 4 4 chr1 5356589 5363302 a 0 - 5 5 chr1 6988975 6995688 a 0 - 6 6 chr1 8197569 8204282 a 0 - 7 7 chr14 7810301 7817014 a 0 + 8 8 chr22 8988597 8995310 a 0 - 9 9 chr6 1920717 1927430 a 0 + 10 10 chr9 5275053 5281766 a 0 + 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9180771 | 9187484 | a | 0 | + | | chr1 | 7067807 | 7074520 | a | 0 | + | | chr1 | 1 | 6714 | a | 0 | + | | chr1 | 4452539 | 4456203 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr6 | 1920717 | 1927430 | a | 0 | + | | chr9 | 5275053 | 5281766 | a | 0 | + | | chr14 | 7810301 | 7817014 | a | 0 | + | | chr22 | 8988597 | 8995310 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2452596 | 2459460 | a | 0 | - | | chr7 | 7599354 | 7607354 | a | 0 | + | | chr12 | 8807105 | 8809153 | a | 0 | - | | chr15 | 3613396 | 3614478 | a | 0 | - | | chr20 | 3793669 | 3800761 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmphcor0jgy/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2452596 2459460 a 0 - 1 1 chr12 8807105 8809153 a 0 - 2 2 chr15 3613396 3614478 a 0 - 3 3 chr20 3793669 3800761 a 0 + 4 4 chr7 7599354 7607354 a 0 + 5 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2452596 | 2459460 | a | 0 | - | | chr7 | 7599354 | 7607354 | a | 0 | + | | chr12 | 8807105 | 8809153 | a | 0 | - | | chr15 | 3613396 | 3614478 | a | 0 | - | | chr20 | 3793669 | 3800761 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7189302 | 7198647 | a | 0 | + | | chr1 | 2019718 | 2023517 | a | 0 | + | | chr1 | 2019718 | 2023638 | a | 0 | + | | chr1 | 2019718 | 2028975 | a | 0 | - | | chr2 | 5790268 | 5792796 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp5v6x4bds/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2019718 2023517 a 0 + 1 1 chr1 2019718 2023638 a 0 + 1 2 chr1 7189302 7198647 a 0 + 2 3 chr1 2019718 2028975 a 0 - 3 4 chr2 5790268 5792796 a 0 + 4 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7189302 | 7198647 | a | 0 | + | | chr1 | 2019718 | 2023517 | a | 0 | + | | chr1 | 2019718 | 2023638 | a | 0 | + | | chr1 | 2019718 | 2028975 | a | 0 | - | | chr2 | 5790268 | 5792796 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5024054 | 5028693 | a | 0 | + | | chr1 | 9954193 | 9957295 | a | 0 | + | | chr1 | 4261857 | 4267423 | a | 0 | + | | chr1 | 2096343 | 2096505 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr4 | 5720161 | 5723155 | a | 0 | + | | chr19 | 1614580 | 1616976 | a | 0 | - | | chr21 | 9954193 | 9958643 | a | 0 | + | | chrX | 257495 | 261945 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp5yint_02/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 4261857 4267423 a 0 + 1 1 chr1 5024054 5028693 a 0 + 2 2 chr1 9954193 9957295 a 0 + 3 3 chr1 2096343 2096505 a 0 - 4 4 chr1 9954193 9954532 a 0 - 5 5 chr1 9954193 9958643 a 0 - 5 6 chr19 1614580 1616976 a 0 - 6 7 chr21 9954193 9958643 a 0 + 7 8 chr3 2782019 2783961 a 0 + 8 9 chr4 5720161 5723155 a 0 + 9 10 chrX 257495 261945 a 0 + 10 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5024054 | 5028693 | a | 0 | + | | chr1 | 9954193 | 9957295 | a | 0 | + | | chr1 | 4261857 | 4267423 | a | 0 | + | | chr1 | 2096343 | 2096505 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr4 | 5720161 | 5723155 | a | 0 | + | | chr19 | 1614580 | 1616976 | a | 0 | - | | chr21 | 9954193 | 9958643 | a | 0 | + | | chrX | 257495 | 261945 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 10000000 | 10008469 | a | 0 | + | | chr1 | 3884473 | 3884945 | a | 0 | + | | chr1 | 2623336 | 2623843 | a | 0 | - | | chr18 | 506198 | 514932 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpym411xkx/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 3884473 3884945 a 0 + 1 1 chr1 10000000 10008469 a 0 + 2 2 chr1 2623336 2623843 a 0 - 3 3 chr18 506198 514932 a 0 + 4 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 10000000 | 10008469 | a | 0 | + | | chr1 | 3884473 | 3884945 | a | 0 | + | | chr1 | 2623336 | 2623843 | a | 0 | - | | chr18 | 506198 | 514932 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9491215 | 9494316 | a | 0 | + | | chr1 | 1711620 | 1718217 | a | 0 | - | | chr1 | 5124122 | 5133198 | a | 0 | - | | chr4 | 5987152 | 5996137 | a | 0 | - | | chr9 | 1324013 | 1328548 | a | 0 | - | | chr21 | 8374657 | 8382424 | a | 0 | + | | chr22 | 1552369 | 1554454 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 7 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmppshrv0jv/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 9491215 9494316 a 0 + 1 1 chr1 1711620 1718217 a 0 - 2 2 chr1 5124122 5133198 a 0 - 3 3 chr21 8374657 8382424 a 0 + 4 4 chr22 1552369 1554454 a 0 + 5 5 chr4 5987152 5996137 a 0 - 6 6 chr9 1324013 1328548 a 0 - 7 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9491215 | 9494316 | a | 0 | + | | chr1 | 1711620 | 1718217 | a | 0 | - | | chr1 | 5124122 | 5133198 | a | 0 | - | | chr4 | 5987152 | 5996137 | a | 0 | - | | chr9 | 1324013 | 1328548 | a | 0 | - | | chr21 | 8374657 | 8382424 | a | 0 | + | | chr22 | 1552369 | 1554454 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 7 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6624767 | 6625063 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpba9ep8h3/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 6624767 6625063 a 0 - 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6624767 | 6625063 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4094890 | 4096341 | a | 0 | + | | chr1 | 7196469 | 7202673 | a | 0 | - | | chr1 | 226437 | 230323 | a | 0 | - | | chr6 | 3080807 | 3089087 | a | 0 | - | | chr9 | 9999999 | 10006203 | a | 0 | + | | chr13 | 2 | 2019 | a | 0 | - | | chr14 | 4079155 | 4089154 | a | 0 | + | | chrM | 6035179 | 6035364 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 8 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpx9__q5e8/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 4094890 4096341 a 0 + 1 1 chr1 226437 230323 a 0 - 2 2 chr1 7196469 7202673 a 0 - 3 3 chr13 2 2019 a 0 - 4 4 chr14 4079155 4089154 a 0 + 5 5 chr6 3080807 3089087 a 0 - 6 6 chr9 9999999 10006203 a 0 + 7 7 chrM 6035179 6035364 a 0 - 8 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4094890 | 4096341 | a | 0 | + | | chr1 | 7196469 | 7202673 | a | 0 | - | | chr1 | 226437 | 230323 | a | 0 | - | | chr6 | 3080807 | 3089087 | a | 0 | - | | chr9 | 9999999 | 10006203 | a | 0 | + | | chr13 | 2 | 2019 | a | 0 | - | | chr14 | 4079155 | 4089154 | a | 0 | + | | chrM | 6035179 | 6035364 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 8 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2307006 | 2315198 | a | 0 | + | | chr1 | 2307006 | 2316959 | a | 0 | + | | chr1 | 2307006 | 2307438 | a | 0 | + | | chr1 | 2307006 | 2314595 | a | 0 | + | | chr1 | 2307006 | 2308922 | a | 0 | + | | chr1 | 2307006 | 2310875 | a | 0 | + | | chr1 | 2307006 | 2310734 | a | 0 | - | | chr1 | 2307006 | 2310189 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 8 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpf52keqmx/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2307006 2307438 a 0 + 1 1 chr1 2307006 2308922 a 0 + 1 2 chr1 2307006 2310875 a 0 + 1 3 chr1 2307006 2314595 a 0 + 1 4 chr1 2307006 2315198 a 0 + 1 5 chr1 2307006 2316959 a 0 + 1 6 chr1 2307006 2310189 a 0 - 2 7 chr1 2307006 2310734 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2307006 | 2315198 | a | 0 | + | | chr1 | 2307006 | 2316959 | a | 0 | + | | chr1 | 2307006 | 2307438 | a | 0 | + | | chr1 | 2307006 | 2314595 | a | 0 | + | | chr1 | 2307006 | 2308922 | a | 0 | + | | chr1 | 2307006 | 2310875 | a | 0 | + | | chr1 | 2307006 | 2310734 | a | 0 | - | | chr1 | 2307006 | 2310189 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 8 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9419398 | 9429398 | a | 0 | - | | chr1 | 3437315 | 3443776 | a | 0 | - | | chr1 | 3437315 | 3443085 | a | 0 | - | | chr1 | 3437315 | 3446365 | a | 0 | - | | chr3 | 3437315 | 3442523 | a | 0 | - | | chr9 | 3437315 | 3445024 | a | 0 | - | | chr11 | 5813226 | 5815412 | a | 0 | - | | chr13 | 5815075 | 5818211 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 8 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpxpa1wehx/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 3437315 3443085 a 0 - 1 1 chr1 3437315 3443776 a 0 - 1 2 chr1 3437315 3446365 a 0 - 1 3 chr1 9419398 9429398 a 0 - 2 4 chr11 5813226 5815412 a 0 - 3 5 chr13 5815075 5818211 a 0 - 4 6 chr3 3437315 3442523 a 0 - 5 7 chr9 3437315 3445024 a 0 - 6 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9419398 | 9429398 | a | 0 | - | | chr1 | 3437315 | 3443776 | a | 0 | - | | chr1 | 3437315 | 3443085 | a | 0 | - | | chr1 | 3437315 | 3446365 | a | 0 | - | | chr3 | 3437315 | 3442523 | a | 0 | - | | chr9 | 3437315 | 3445024 | a | 0 | - | | chr11 | 5813226 | 5815412 | a | 0 | - | | chr13 | 5815075 | 5818211 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 8 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2190824 | 2193688 | a | 0 | + | | chr1 | 1 | 1968 | a | 0 | + | | chr1 | 4331650 | 4332739 | a | 0 | - | | chr1 | 4331650 | 4341427 | a | 0 | - | | chr1 | 9247198 | 9256492 | a | 0 | - | | chr7 | 5310737 | 5312032 | a | 0 | - | | chr9 | 4331650 | 4337950 | a | 0 | + | | chr13 | 4331650 | 4332205 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 8 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpwx3daz_z/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 1968 a 0 + 1 1 chr1 2190824 2193688 a 0 + 2 2 chr1 4331650 4332739 a 0 - 3 3 chr1 4331650 4341427 a 0 - 3 4 chr1 9247198 9256492 a 0 - 4 5 chr13 4331650 4332205 a 0 + 5 6 chr7 5310737 5312032 a 0 - 6 7 chr9 4331650 4337950 a 0 + 7 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2190824 | 2193688 | a | 0 | + | | chr1 | 1 | 1968 | a | 0 | + | | chr1 | 4331650 | 4332739 | a | 0 | - | | chr1 | 4331650 | 4341427 | a | 0 | - | | chr1 | 9247198 | 9256492 | a | 0 | - | | chr7 | 5310737 | 5312032 | a | 0 | - | | chr9 | 4331650 | 4337950 | a | 0 | + | | chr13 | 4331650 | 4332205 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 8 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7871216 | 7877081 | a | 0 | + | | chr1 | 8534365 | 8540230 | a | 0 | + | | chr1 | 484332 | 490197 | a | 0 | + | | chr1 | 7314828 | 7320693 | a | 0 | + | | chr4 | 4379464 | 4385329 | a | 0 | + | | chr5 | 9468528 | 9474393 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpfbp5wavv/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 484332 490197 a 0 + 1 1 chr1 7314828 7320693 a 0 + 2 2 chr1 7871216 7877081 a 0 + 3 3 chr1 8534365 8540230 a 0 + 4 4 chr4 4379464 4385329 a 0 + 5 5 chr5 9468528 9474393 a 0 + 6 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7871216 | 7877081 | a | 0 | + | | chr1 | 8534365 | 8540230 | a | 0 | + | | chr1 | 484332 | 490197 | a | 0 | + | | chr1 | 7314828 | 7320693 | a | 0 | + | | chr4 | 4379464 | 4385329 | a | 0 | + | | chr5 | 9468528 | 9474393 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1557649 | 1559619 | a | 0 | + | | chr1 | 2464398 | 2469310 | a | 0 | + | | chr1 | 2641140 | 2643110 | a | 0 | - | | chr1 | 4669083 | 4673577 | a | 0 | - | | chr17 | 4669083 | 4669915 | a | 0 | + | | chr20 | 4669083 | 4675664 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpom4z3cu9/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1557649 1559619 a 0 + 1 1 chr1 2464398 2469310 a 0 + 2 2 chr1 2641140 2643110 a 0 - 3 3 chr1 4669083 4673577 a 0 - 4 4 chr17 4669083 4669915 a 0 + 5 5 chr20 4669083 4675664 a 0 + 6 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1557649 | 1559619 | a | 0 | + | | chr1 | 2464398 | 2469310 | a | 0 | + | | chr1 | 2641140 | 2643110 | a | 0 | - | | chr1 | 4669083 | 4673577 | a | 0 | - | | chr17 | 4669083 | 4669915 | a | 0 | + | | chr20 | 4669083 | 4675664 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9040925 | 9047999 | a | 0 | + | | chr1 | 3656175 | 3664657 | a | 0 | - | | chr15 | 2505231 | 2514806 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpcjsyuflj/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 9040925 9047999 a 0 + 1 1 chr1 3656175 3664657 a 0 - 2 2 chr15 2505231 2514806 a 0 + 3 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9040925 | 9047999 | a | 0 | + | | chr1 | 3656175 | 3664657 | a | 0 | - | | chr15 | 2505231 | 2514806 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5472164 | 5472760 | a | 0 | + | | chr1 | 5472164 | 5472760 | a | 0 | + | | chr1 | 5472164 | 5472760 | a | 0 | + | | chr1 | 5472164 | 5472760 | a | 0 | + | | chr1 | 5472164 | 5472760 | a | 0 | + | | chr1 | 5472164 | 5472760 | a | 0 | - | | chr1 | 5472164 | 5472760 | a | 0 | - | | chr1 | 5472164 | 5475707 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 8 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp_o9uiok5/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 5472164 5472760 a 0 + 1 1 chr1 5472164 5472760 a 0 + 1 2 chr1 5472164 5472760 a 0 + 1 3 chr1 5472164 5472760 a 0 + 1 4 chr1 5472164 5472760 a 0 + 1 5 chr1 5472164 5472760 a 0 - 2 6 chr1 5472164 5472760 a 0 - 2 7 chr1 5472164 5475707 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5472164 | 5472760 | a | 0 | + | | chr1 | 5472164 | 5472760 | a | 0 | + | | chr1 | 5472164 | 5472760 | a | 0 | + | | chr1 | 5472164 | 5472760 | a | 0 | + | | chr1 | 5472164 | 5472760 | a | 0 | + | | chr1 | 5472164 | 5472760 | a | 0 | - | | chr1 | 5472164 | 5472760 | a | 0 | - | | chr1 | 5472164 | 5475707 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 8 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8414514 | 8416612 | a | 0 | + | | chr1 | 7640381 | 7644674 | a | 0 | + | | chr1 | 5416035 | 5423200 | a | 0 | + | | chr1 | 8893788 | 8898557 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr1 | 5416035 | 5423200 | a | 0 | + | | chr1 | 8893788 | 8898557 | a | 0 | - | | chr1 | 8910252 | 8920238 | a | 0 | - | | chr1 | 1 | 3625 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 9 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpxojzwm_5/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 5416035 5423200 a 0 + 1 1 chr1 7640381 7644674 a 0 + 2 2 chr1 8414514 8416612 a 0 + 3 3 chr1 1 3625 a 0 - 4 4 chr1 8893788 8898557 a 0 - 5 5 chr1 8910252 8920238 a 0 - 6 6 chr19 2853298 2860945 a 0 + 7 7 chr19 4062936 4064993 a 0 - 8 8 chrX 7131320 7141319 a 0 + 9 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8414514 | 8416612 | a | 0 | + | | chr1 | 7640381 | 7644674 | a | 0 | + | | chr1 | 5416035 | 5423200 | a | 0 | + | | chr1 | 8893788 | 8898557 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr1 | 5416035 | 5423200 | a | 0 | + | | chr1 | 8893788 | 8898557 | a | 0 | - | | chr1 | 8910252 | 8920238 | a | 0 | - | | chr1 | 1 | 3625 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 9 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8100350 | 8103162 | a | 0 | + | | chr3 | 7515716 | 7522523 | a | 0 | + | | chr3 | 5258377 | 5263514 | a | 0 | - | | chr21 | 6533159 | 6537913 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpc4m020pr/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 8100350 8103162 a 0 + 1 1 chr21 6533159 6537913 a 0 + 2 2 chr3 7515716 7522523 a 0 + 3 3 chr3 5258377 5263514 a 0 - 4 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8100350 | 8103162 | a | 0 | + | | chr3 | 7515716 | 7522523 | a | 0 | + | | chr3 | 5258377 | 5263514 | a | 0 | - | | chr21 | 6533159 | 6537913 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2482240 | 2487604 | a | 0 | + | | chr1 | 2304256 | 2307970 | a | 0 | + | | chr8 | 3887502 | 3893116 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpy3c7y72z/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2304256 2307970 a 0 + 1 1 chr1 2482240 2487604 a 0 + 2 2 chr8 3887502 3893116 a 0 + 3 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2482240 | 2487604 | a | 0 | + | | chr1 | 2304256 | 2307970 | a | 0 | + | | chr8 | 3887502 | 3893116 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 335 | a | 0 | + | | chr1 | 8160180 | 8170121 | a | 0 | + | | chr1 | 1 | 9942 | a | 0 | + | | chr1 | 1 | 9942 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr1 | 1 | 9942 | a | 0 | + | | chr1 | 1 | 9942 | a | 0 | - | | chr1 | 8344579 | 8345677 | a | 0 | - | | chr1 | 4610738 | 4620679 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 9 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpuy81rsl9/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 335 a 0 + 1 1 chr1 1 9942 a 0 + 1 2 chr1 8160180 8170121 a 0 + 2 3 chr1 1 9942 a 0 - 3 4 chr1 4610738 4620679 a 0 - 4 5 chr1 8344579 8345677 a 0 - 5 6 chr14 1523505 1533446 a 0 + 6 7 chr19 1 9942 a 0 - 7 8 chr7 1 1653 a 0 - 8 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 335 | a | 0 | + | | chr1 | 8160180 | 8170121 | a | 0 | + | | chr1 | 1 | 9942 | a | 0 | + | | chr1 | 1 | 9942 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr1 | 1 | 9942 | a | 0 | + | | chr1 | 1 | 9942 | a | 0 | - | | chr1 | 8344579 | 8345677 | a | 0 | - | | chr1 | 4610738 | 4620679 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 9 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpfsr2bsoj/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 2 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ________________________________ test_windows2 _________________________________ [gw0] linux -- Python 3.12.6 /usr/bin/python3.12 def test_windows2(): c = """Chromosome Start End Count 0 chr1 10200 10400 7 1 chr1 10400 10600 7 2 chr1 51400 51600 1 3 chr1 51600 51800 3 4 chr1 51800 52000 3""" df = pd.read_csv(StringIO(c), sep=r"\s+", nrows=5) # df.End -= 1 gr = pr.PyRanges(df) print(gr) > result = gr.tile(200) tests/windows/test_windows.py:48: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ pyranges/pyranges.py:4649: in tile df = pyrange_apply_single(_tiles, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/windows.py:40: in _tiles idxs, starts, ends = maketiles(df.index.values, df.Start.values, sorted_nearest/src/tiles.pyx:24: in sorted_nearest.src.tiles.maketiles ??? _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'long' but got 'long long' sorted_nearest/src/tiles.pyx:48: ValueError ----------------------------- Captured stdout call ----------------------------- +--------------+-----------+-----------+-----------+ | Chromosome | Start | End | Count | | (category) | (int32) | (int32) | (int64) | |--------------+-----------+-----------+-----------| | chr1 | 10200 | 10400 | 7 | | chr1 | 10400 | 10600 | 7 | | chr1 | 51400 | 51600 | 1 | | chr1 | 51600 | 51800 | 3 | | chr1 | 51800 | 52000 | 3 | +--------------+-----------+-----------+-----------+ Unstranded PyRanges object has 5 rows and 4 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome. _________________________________ test_windows _________________________________ [gw10] linux -- Python 3.12.6 /usr/bin/python3.12 @pytest.mark.bedtools > @settings( max_examples=max_examples, print_blob=True, deadline=deadline, suppress_health_check=HealthCheck.all()) tests/test_unary.py:230: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_unary.py:259: in test_windows result = gr.window(10)["Chromosome Start End".split()].unstrand() pyranges/pyranges.py:5485: in window df = pyrange_apply_single(_windows, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/windows.py:11: in _windows idxs, starts, ends = makewindows(df.index.values, df.Start.values, _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_windows( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., # or any other generated value E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2TABAAAKAAC') as a decorator on your test case sorted_nearest/src/windows.pyx:20: Exception ----------------------------- Captured stdout call ----------------------------- bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpwl8_u4dv/f1.bed) bedtools_df Chromosome Start End 0 chr1 1 2 bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpvwo3s375/f1.bed) bedtools_df Chromosome Start End 0 chr1 1142023 1142033 1 chr1 1142033 1142043 2 chr1 1142043 1142053 3 chr1 1142053 1142063 4 chr1 1142063 1142073 ... ... ... ... 4976 chrY 9833542 9833552 4977 chrY 9833552 9833562 4978 chrY 9833562 9833572 4979 chrY 9833572 9833582 4980 chrY 9833582 9833591 [4981 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpdm7ui8sx/f1.bed) bedtools_df Chromosome Start End 0 chr1 1142023 1142029 1 chr1 2037468 2037474 2 chr1 3991283 3991289 3 chr1 5883397 5883403 4 chr1 7144814 7144820 5 chr1 8956715 8956721 6 chr1 9753509 9753515 7 chr12 8777892 8777898 8 chr18 5747121 5747127 9 chrY 9829512 9829518 bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpytsbrlew/f1.bed) bedtools_df Chromosome Start End 0 chr1 1142023 1142029 1 chr1 2037468 2037474 2 chr1 3991283 3991289 3 chr1 5883397 5883403 4 chr1 7144814 7144820 5 chr1 9753509 9753515 6 chr12 8777892 8777898 7 chr18 5747121 5747127 8 chr18 8956715 8956721 9 chrY 9829512 9829518 bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpr8zv7dts/f1.bed) bedtools_df Chromosome Start End 0 chr1 2 12 1 chr1 12 22 2 chr1 22 32 3 chr1 32 42 4 chr1 42 52 ... ... ... ... 3417 chr1 7912 7922 3418 chr1 7922 7932 3419 chr1 7932 7942 3420 chr1 7942 7952 3421 chr1 7952 7961 [3422 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpdi73o4n3/f1.bed) bedtools_df Chromosome Start End 0 chr1 65537 65547 1 chr1 65547 65557 2 chr1 65557 65567 3 chr1 65567 65577 4 chr1 65577 65587 ... ... ... ... 3160 chr1 71557 71567 3161 chr1 71567 71577 3162 chr1 71577 71587 3163 chr1 71587 71597 3164 chr1 71597 71603 [3165 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpramr758h/f1.bed) bedtools_df Chromosome Start End 0 chr1 65537 65547 1 chr1 65547 65557 2 chr1 65557 65567 3 chr1 65567 65577 4 chr1 65577 65587 ... ... ... ... 3160 chr1 71557 71567 3161 chr1 71567 71577 3162 chr1 71577 71587 3163 chr1 71587 71597 3164 chr1 71597 71603 [3165 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpcvuisawx/f1.bed) bedtools_df Chromosome Start End 0 chr1 65537 65547 1 chr1 65547 65557 2 chr1 65557 65567 3 chr1 65567 65577 4 chr1 65577 65587 ... ... ... ... 3160 chr1 71557 71567 3161 chr1 71567 71577 3162 chr1 71577 71587 3163 chr1 71587 71597 3164 chr1 71597 71603 [3165 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp4lbw7jim/f1.bed) bedtools_df Chromosome Start End 0 chr1 2109133 2109143 1 chr1 2109143 2109153 2 chr1 2109153 2109163 3 chr1 2109163 2109173 4 chr1 2109173 2109183 ... ... ... ... 5682 chr5 8788182 8788192 5683 chr5 8788192 8788202 5684 chr5 8788202 8788212 5685 chr5 8788212 8788222 5686 chr5 8788222 8788228 [5687 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp8hgdkeao/f1.bed) bedtools_df Chromosome Start End 0 chr1 65537 65539 1 chr12 65537 65539 2 chr14 4 14 3 chr14 14 24 4 chr14 24 34 5 chr14 34 44 6 chr14 44 54 7 chr14 54 64 8 chr14 64 74 9 chr14 74 84 10 chr14 84 94 11 chr14 94 104 12 chr14 104 114 13 chr14 114 124 14 chr14 124 134 15 chr14 134 144 16 chr14 144 154 17 chr14 154 164 18 chr14 164 174 19 chr14 174 184 20 chr14 184 194 21 chr14 194 204 22 chr14 204 214 23 chr14 214 224 24 chr14 224 234 25 chr14 234 244 26 chr14 244 254 27 chr14 254 261 28 chr2 65537 65539 29 chr2 65537 65539 30 chr2 65537 65539 31 chr2 65537 65539 32 chr2 65537 65539 33 chr2 65537 65539 34 chr2 65537 65539 bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp0gmnrt63/f1.bed) bedtools_df Chromosome Start End 0 chr1 1 2 bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp2vtbyt1i/f1.bed) bedtools_df Chromosome Start End 0 chr1 1 2 bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmprovbkb_l/f1.bed) bedtools_df Chromosome Start End 0 chr1 1 2 bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpjwmeh29o/f1.bed) bedtools_df Chromosome Start End 0 chr1 1 2 bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpuqmv3j8s/f1.bed) bedtools_df Chromosome Start End 0 chr1 1 2 bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpmale0mmc/f1.bed) bedtools_df Chromosome Start End 0 chr1 4130308 4130318 1 chr1 4130318 4130328 2 chr1 4130328 4130338 3 chr1 4130338 4130348 4 chr1 4130348 4130358 ... ... ... ... 1029 chr14 2908817 2908827 1030 chr14 2908827 2908837 1031 chr14 2908837 2908847 1032 chr14 2908847 2908857 1033 chr14 2908857 2908863 [1034 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpqw23lt0o/f1.bed) bedtools_df Chromosome Start End 0 chr1 1 11 1 chr1 11 21 2 chr1 21 31 3 chr1 31 41 4 chr1 41 51 ... ... ... ... 2141 chr15 4629623 4629633 2142 chr15 4629633 4629643 2143 chr15 4629643 4629653 2144 chr15 4629653 4629663 2145 chr15 4629663 4629668 [2146 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpc8ur0pcb/f1.bed) bedtools_df Chromosome Start End 0 chr1 2290238 2290248 1 chr1 2290248 2290258 2 chr1 2290258 2290268 3 chr1 2290268 2290278 4 chr1 2290278 2290288 .. ... ... ... 916 chr1 4355365 4355375 917 chr1 4355375 4355385 918 chr1 4355385 4355395 919 chr1 4355395 4355405 920 chr1 4355405 4355409 [921 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp8hmac3am/f1.bed) bedtools_df Chromosome Start End 0 chr1 4196420 4196430 1 chr1 4196430 4196440 2 chr1 4196440 4196450 3 chr1 4196450 4196460 4 chr1 4196460 4196470 ... ... ... ... 6502 chrY 2944497 2944507 6503 chrY 2944507 2944517 6504 chrY 2944517 2944527 6505 chrY 2944527 2944537 6506 chrY 2944537 2944538 [6507 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpqh18pv8n/f1.bed) bedtools_df Chromosome Start End 0 chr1 185448 185458 1 chr1 185458 185468 2 chr1 185468 185478 3 chr1 185478 185488 4 chr1 185488 185498 ... ... ... ... 4594 chr16 6256730 6256740 4595 chr16 6256740 6256750 4596 chr16 6256750 6256760 4597 chr16 6256760 6256770 4598 chr16 6256770 6256777 [4599 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpiqw44vq_/f1.bed) bedtools_df Chromosome Start End 0 chr1 1998632 1998642 1 chr1 1998642 1998652 2 chr1 1998652 1998662 3 chr1 1998662 1998672 4 chr1 1998672 1998682 ... ... ... ... 2774 chrM 6129616 6129626 2775 chrM 6129626 6129636 2776 chrM 6129636 6129646 2777 chrM 6129646 6129656 2778 chrM 6129656 6129658 [2779 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpko90zg7p/f1.bed) bedtools_df Chromosome Start End 0 chr1 3975860 3975861 1 chr1 3975860 3975870 2 chr1 3975870 3975880 3 chr1 3975880 3975890 4 chr1 3975890 3975900 ... ... ... ... 3738 chrX 3980690 3980700 3739 chrX 3980700 3980710 3740 chrX 3980710 3980720 3741 chrX 3980720 3980730 3742 chrX 3980730 3980731 [3743 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmps8k75fp2/f1.bed) bedtools_df Chromosome Start End 0 chr1 645868 645878 1 chr1 645878 645888 2 chr1 645888 645898 3 chr1 645898 645908 4 chr1 645908 645918 ... ... ... ... 10214 chr8 586737 586747 10215 chr8 586747 586757 10216 chr8 586757 586767 10217 chr8 586767 586777 10218 chr8 586777 586787 [10219 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpckb_yovh/f1.bed) bedtools_df Chromosome Start End 0 chr1 4062724 4062734 1 chr1 4062734 4062744 2 chr1 4062744 4062754 3 chr1 4062754 4062764 4 chr1 4062764 4062774 ... ... ... ... 6291 chrM 9051298 9051308 6292 chrM 9051308 9051318 6293 chrM 9051318 9051328 6294 chrM 9051328 9051338 6295 chrM 9051338 9051348 [6296 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmprclu1fj1/f1.bed) bedtools_df Chromosome Start End 0 chr1 2077465 2077475 1 chr1 2077475 2077485 2 chr1 2077485 2077495 3 chr1 2077495 2077505 4 chr1 2077505 2077515 ... ... ... ... 4527 chr5 4314833 4314843 4528 chr5 4314843 4314853 4529 chr5 4314853 4314863 4530 chr5 4314863 4314873 4531 chr5 4314873 4314878 [4532 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmprpi_njz9/f1.bed) bedtools_df Chromosome Start End 0 chr10 1183935 1183945 1 chr10 1183945 1183955 2 chr10 1183955 1183965 3 chr10 1183965 1183975 4 chr10 1183975 1183985 ... ... ... ... 2004 chr21 189467 189477 2005 chr21 189477 189487 2006 chr21 189487 189497 2007 chr21 189497 189507 2008 chr21 189507 189508 [2009 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpi3nh4ls7/f1.bed) bedtools_df Chromosome Start End 0 chr1 2688539 2688549 1 chr1 2688549 2688559 2 chr1 2688559 2688569 3 chr1 2688569 2688579 4 chr1 2688579 2688589 ... ... ... ... 4414 chrM 6103426 6103436 4415 chrM 6103436 6103446 4416 chrM 6103446 6103456 4417 chrM 6103456 6103466 4418 chrM 6103466 6103467 [4419 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpulc1umer/f1.bed) bedtools_df Chromosome Start End 0 chr1 9715074 9715084 1 chr1 9715084 9715094 2 chr1 9715094 9715104 3 chr1 9715104 9715114 4 chr1 9715114 9715124 .. ... ... ... 467 chr1 9719744 9719754 468 chr1 9719754 9719764 469 chr1 9719764 9719774 470 chr1 9719774 9719784 471 chr1 9990187 9990189 [472 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpvtill2ej/f1.bed) bedtools_df Chromosome Start End 0 chr1 1616770 1616780 1 chr1 1616780 1616790 2 chr1 1616790 1616800 3 chr1 1616800 1616810 4 chr1 1616810 1616820 ... ... ... ... 4555 chrY 3959494 3959504 4556 chrY 3959504 3959514 4557 chrY 3959514 3959524 4558 chrY 3959524 3959534 4559 chrY 3959534 3959541 [4560 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpl7acger0/f1.bed) bedtools_df Chromosome Start End 0 chr1 1177996 1178006 1 chr1 1178006 1178016 2 chr1 1178016 1178026 3 chr1 1178026 1178036 4 chr1 1178036 1178046 .. ... ... ... 927 chr1 5634056 5634066 928 chr1 5634066 5634076 929 chr1 5634076 5634086 930 chr1 5634086 5634096 931 chr1 5634096 5634098 [932 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp66342ctz/f1.bed) bedtools_df Chromosome Start End 0 chr1 2 12 1 chr1 12 22 2 chr1 22 32 3 chr1 32 42 4 chr1 42 52 .. ... ... ... 260 chr18 6526522 6526532 261 chr18 6526532 6526542 262 chr18 6526542 6526552 263 chr18 6526552 6526555 264 chr4 6417728 6417730 [265 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp_pz1j5hl/f1.bed) bedtools_df Chromosome Start End 0 chr1 4587081 4587091 1 chr1 4587091 4587101 2 chr1 4587101 4587111 3 chr1 4587111 4587121 4 chr1 4587121 4587131 ... ... ... ... 2733 chr12 7552763 7552773 2734 chr12 7552773 7552783 2735 chr12 7552783 7552793 2736 chr12 7552793 7552803 2737 chr12 7552803 7552813 [2738 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmppuujzgqd/f1.bed) bedtools_df Chromosome Start End 0 chr10 1590786 1590796 1 chr10 1590796 1590806 2 chr10 1590806 1590816 3 chr10 1590816 1590826 4 chr10 1590826 1590836 ... ... ... ... 3917 chr14 2508728 2508738 3918 chr14 2508738 2508748 3919 chr14 2508748 2508758 3920 chr14 2508758 2508768 3921 chr14 2508768 2508769 [3922 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp0nua18ar/f1.bed) bedtools_df Chromosome Start End 0 chr1 3535333 3535334 1 chr1 9163049 9163059 2 chr1 9163059 9163069 3 chr1 9163069 9163079 4 chr1 9163079 9163089 ... ... ... ... 4609 chr5 603546 603556 4610 chr5 603556 603566 4611 chr5 603566 603576 4612 chr5 603576 603586 4613 chr5 603586 603588 [4614 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpi2akc41y/f1.bed) bedtools_df Chromosome Start End 0 chr1 6959965 6959975 1 chr1 6959975 6959985 2 chr1 6959985 6959995 3 chr1 6959995 6960005 4 chr1 6960005 6960015 ... ... ... ... 1436 chrM 3288491 3288501 1437 chrM 3288501 3288511 1438 chrM 3288511 3288521 1439 chrM 3288521 3288531 1440 chrM 3288531 3288539 [1441 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpqwcy3f8i/f1.bed) bedtools_df Chromosome Start End 0 chr1 4971439 4971449 1 chr1 4971449 4971459 2 chr1 4971459 4971469 3 chr1 4971469 4971479 4 chr1 4971479 4971489 .. ... ... ... 636 chr1 4977799 4977809 637 chr1 4977809 4977819 638 chr1 4977819 4977829 639 chr1 4977829 4977839 640 chr1 4977839 4977840 [641 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmphu67uuyk/f1.bed) bedtools_df Chromosome Start End 0 chr8 6473955 6473965 1 chr8 6473965 6473975 2 chr8 6473975 6473985 3 chr8 6473985 6473995 4 chr8 6473995 6474005 .. ... ... ... 818 chr8 6482135 6482145 819 chr8 6482145 6482155 820 chr8 6482155 6482165 821 chr8 6482165 6482175 822 chr8 6482175 6482182 [823 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp0vq9z3l_/f1.bed) bedtools_df Chromosome Start End 0 chr1 3610192 3610202 1 chr1 3610202 3610212 2 chr1 3610212 3610222 3 chr1 3610222 3610232 4 chr1 3610232 3610242 ... ... ... ... 7134 chrM 1746110 1746120 7135 chrM 1746120 1746130 7136 chrM 1746130 1746140 7137 chrM 1746140 1746150 7138 chrM 1746150 1746157 [7139 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpppk9him_/f1.bed) bedtools_df Chromosome Start End 0 chr1 1471721 1471731 1 chr1 1471731 1471741 2 chr1 1471741 1471751 3 chr1 1471751 1471761 4 chr1 1471761 1471771 ... ... ... ... 1228 chr1 7979499 7979509 1229 chr1 7979509 7979519 1230 chr1 7979519 7979529 1231 chr1 7979529 7979539 1232 chr1 7979539 7979540 [1233 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpnua40hiu/f1.bed) bedtools_df Chromosome Start End 0 chr1 1966554 1966564 1 chr1 1966564 1966574 2 chr1 1966574 1966584 3 chr1 1966584 1966594 4 chr1 1966594 1966604 ... ... ... ... 3500 chrX 7819469 7819479 3501 chrX 7819479 7819489 3502 chrX 7819489 7819499 3503 chrX 7819499 7819509 3504 chrX 7819509 7819517 [3505 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmptu65qzoe/f1.bed) bedtools_df Chromosome Start End 0 chr1 3943557 3943567 1 chr1 3943567 3943577 2 chr1 3943577 3943587 3 chr1 3943587 3943597 4 chr1 3943597 3943607 ... ... ... ... 2109 chr1 6816106 6816116 2110 chr1 6816116 6816126 2111 chr1 6816126 6816136 2112 chr1 6816136 6816146 2113 chr1 6816146 6816155 [2114 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpuy3j44ln/f1.bed) bedtools_df Chromosome Start End 0 chr1 3755739 3755749 1 chr1 3755749 3755759 2 chr1 3755759 3755769 3 chr1 3755769 3755779 4 chr1 3755779 3755789 ... ... ... ... 4214 chrY 3757229 3757239 4215 chrY 3757239 3757249 4216 chrY 3757249 3757259 4217 chrY 3757259 3757269 4218 chrY 3757269 3757277 [4219 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp3a5ld9x1/f1.bed) bedtools_df Chromosome Start End 0 chr1 2399420 2399430 1 chr1 2399430 2399440 2 chr1 2399440 2399450 3 chr1 2399450 2399460 4 chr1 2399460 2399470 ... ... ... ... 1270 chr1 2406530 2406540 1271 chr1 2406540 2406550 1272 chr1 2406550 2406560 1273 chr1 2406560 2406570 1274 chr1 2406570 2406578 [1275 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp4vzjrtgy/f1.bed) bedtools_df Chromosome Start End 0 chr2 387914 387924 1 chr2 387924 387934 2 chr2 387934 387944 3 chr2 387944 387954 4 chr2 387954 387964 .. ... ... ... 453 chr2 392444 392454 454 chr2 392454 392464 455 chr2 392464 392474 456 chr2 392474 392484 457 chr2 392484 392490 [458 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpr0jy_85x/f1.bed) bedtools_df Chromosome Start End 0 chr5 9020430 9020440 1 chr5 9020440 9020450 2 chr5 9020450 9020460 3 chr5 9020460 9020470 4 chr5 9020470 9020480 .. ... ... ... 80 chr5 9021230 9021240 81 chr5 9021240 9021250 82 chr5 9021250 9021260 83 chr5 9021260 9021270 84 chr5 9021270 9021277 [85 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpggixzco0/f1.bed) bedtools_df Chromosome Start End 0 chr1 1457839 1457849 1 chr1 1457849 1457859 2 chr1 1457859 1457869 3 chr1 1457869 1457879 4 chr1 1457879 1457889 ... ... ... ... 2081 chrY 10004070 10004080 2082 chrY 10004080 10004090 2083 chrY 10004090 10004100 2084 chrY 10004100 10004110 2085 chrY 10004110 10004114 [2086 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpctgpb1wi/f1.bed) bedtools_df Chromosome Start End 0 chr1 431316 431326 1 chr1 431326 431336 2 chr1 431336 431346 3 chr1 431346 431356 4 chr1 431356 431366 ... ... ... ... 6083 chr21 5209492 5209502 6084 chr21 5209502 5209512 6085 chr21 5209512 5209522 6086 chr21 5209522 5209532 6087 chr21 5209532 5209535 [6088 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpz1od370c/f1.bed) bedtools_df Chromosome Start End 0 chr1 9149470 9149480 1 chr1 9149480 9149490 2 chr1 9149490 9149494 3 chr10 9149470 9149480 4 chr10 9149480 9149490 ... ... ... ... 5554 chrM 9150770 9150780 5555 chrM 9150780 9150790 5556 chrM 9150790 9150800 5557 chrM 9150800 9150810 5558 chrM 9150810 9150813 [5559 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpu2_hsdix/f1.bed) bedtools_df Chromosome Start End 0 chr9 1352827 1352837 1 chr9 1352837 1352847 2 chr9 1352847 1352857 3 chr9 1352857 1352867 4 chr9 1352867 1352877 ... ... ... ... 1070 chr9 9372950 9372960 1071 chr9 9372960 9372970 1072 chr9 9372970 9372980 1073 chr9 9372980 9372990 1074 chr9 9372990 9372995 [1075 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpimlmyy02/f1.bed) bedtools_df Chromosome Start End 0 chr1 674401 674411 1 chr1 674411 674421 2 chr1 674421 674431 3 chr1 674431 674441 4 chr1 674441 674451 ... ... ... ... 3406 chr1 8502602 8502612 3407 chr1 8502612 8502622 3408 chr1 8502622 8502632 3409 chr1 8502632 8502642 3410 chr1 8502642 8502647 [3411 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpveb7or1k/f1.bed) bedtools_df Chromosome Start End 0 chr1 6473820 6473830 1 chr1 6473830 6473840 2 chr1 6473840 6473850 3 chr1 6473850 6473860 4 chr1 6473860 6473870 .. ... ... ... 211 chrY 5232948 5232958 212 chrY 5232958 5232968 213 chrY 5232968 5232978 214 chrY 5232978 5232988 215 chrY 5232988 5232998 [216 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpkenvrke6/f1.bed) bedtools_df Chromosome Start End 0 chr9 5758879 5758889 1 chr9 5758889 5758899 2 chr9 5758899 5758909 3 chr9 5758909 5758919 4 chr9 5758919 5758929 .. ... ... ... 720 chr9 5766079 5766089 721 chr9 5766089 5766099 722 chr9 5766099 5766109 723 chr9 5766109 5766119 724 chr9 5766119 5766127 [725 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpdwljn0ne/f1.bed) bedtools_df Chromosome Start End 0 chr1 1955305 1955315 1 chr1 1955315 1955325 2 chr1 1955325 1955335 3 chr1 1955335 1955345 4 chr1 1955345 1955355 ... ... ... ... 5439 chr14 324055 324065 5440 chr14 324065 324075 5441 chr14 324075 324085 5442 chr14 324085 324095 5443 chr14 324095 324099 [5444 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp10yrctez/f1.bed) bedtools_df Chromosome Start End 0 chr16 2128292 2128302 1 chr16 2128302 2128312 2 chr16 2128312 2128322 3 chr16 2128322 2128332 4 chr16 2128332 2128342 5 chr16 2128342 2128352 6 chr16 2128352 2128362 7 chr16 2128362 2128372 8 chr16 2128372 2128382 9 chr16 2128382 2128392 10 chr16 2128392 2128402 11 chr16 2128402 2128412 12 chr16 2128412 2128422 13 chr16 2128422 2128432 14 chr16 2128432 2128442 15 chr16 2128442 2128452 16 chr16 2128452 2128462 17 chr16 2128462 2128472 18 chr16 2128472 2128482 19 chr16 2128482 2128492 20 chr16 2128492 2128502 21 chr16 2128502 2128512 22 chr16 2128512 2128522 23 chr16 2128522 2128532 24 chr16 2128532 2128542 25 chr16 2128542 2128552 26 chr16 2128552 2128562 27 chr16 2128562 2128572 28 chr16 2128572 2128582 29 chr16 2128582 2128591 bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpyx1pktjn/f1.bed) bedtools_df Chromosome Start End 0 chr1 202014 202024 1 chr1 202024 202034 2 chr1 202034 202035 3 chr1 1470781 1470791 4 chr1 1470791 1470801 ... ... ... ... 4058 chr4 891036 891046 4059 chr4 891046 891056 4060 chr4 891056 891066 4061 chr4 891066 891068 4062 chr5 8067953 8067954 [4063 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpjdn_e9cq/f1.bed) bedtools_df Chromosome Start End 0 chr1 1767785 1767795 1 chr1 1767795 1767805 2 chr1 1767805 1767815 3 chr1 1767815 1767825 4 chr1 1767825 1767835 ... ... ... ... 2749 chr8 3644621 3644631 2750 chr8 3644631 3644641 2751 chr8 3644641 3644651 2752 chr8 3644651 3644661 2753 chr8 3644661 3644669 [2754 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp9ky19yt5/f1.bed) bedtools_df Chromosome Start End 0 chr1 5377650 5377660 1 chr1 5377660 5377670 2 chr1 5377670 5377680 3 chr1 5377680 5377690 4 chr1 5377690 5377700 ... ... ... ... 3399 chr20 4382793 4382803 3400 chr20 4382803 4382813 3401 chr20 4382813 4382823 3402 chr20 4382823 4382833 3403 chr20 4382833 4382834 [3404 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp844gtbei/f1.bed) bedtools_df Chromosome Start End 0 chr1 8115360 8115370 1 chr1 8115370 8115380 2 chr1 8115380 8115390 3 chr1 8115390 8115400 4 chr1 8115400 8115410 ... ... ... ... 1979 chr14 3597802 3597812 1980 chr14 3597812 3597822 1981 chr14 3597822 3597832 1982 chr14 3597832 3597842 1983 chr14 3597842 3597852 [1984 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpscddqhm2/f1.bed) bedtools_df Chromosome Start End 0 chr1 6310084 6310094 1 chr1 6310094 6310104 2 chr1 6310104 6310114 3 chr1 6310114 6310124 4 chr1 6310124 6310134 .. ... ... ... 406 chr6 9193535 9193545 407 chr6 9193545 9193555 408 chr6 9193555 9193565 409 chr6 9193565 9193575 410 chr6 9193575 9193583 [411 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp8twa9ue9/f1.bed) bedtools_df Chromosome Start End 0 chr1 4754607 4754617 1 chr1 4754617 4754627 2 chr1 4754627 4754637 3 chr1 4754637 4754647 4 chr1 4754647 4754657 ... ... ... ... 2043 chr11 3339406 3339416 2044 chr11 3339416 3339426 2045 chr11 3339426 3339436 2046 chr11 3339436 3339446 2047 chr11 3339446 3339450 [2048 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp_ejnmtn1/f1.bed) bedtools_df Chromosome Start End 0 chr1 6479467 6479477 1 chr1 6479477 6479487 2 chr1 6479487 6479497 3 chr1 6479497 6479507 4 chr1 6479507 6479517 ... ... ... ... 2546 chr13 8214661 8214671 2547 chr13 8214671 8214681 2548 chr13 8214681 8214691 2549 chr13 8214691 8214699 2550 chr17 5558224 5558225 [2551 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpe453vsa9/f1.bed) bedtools_df Chromosome Start End 0 chr1 6257585 6257595 1 chr1 6257595 6257605 2 chr1 6257605 6257615 3 chr1 6257615 6257625 4 chr1 6257625 6257635 ... ... ... ... 6772 chr7 9872159 9872169 6773 chr7 9872169 9872179 6774 chr7 9872179 9872189 6775 chr7 9872189 9872199 6776 chr7 9872199 9872204 [6777 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp6c9d3kgp/f1.bed) bedtools_df Chromosome Start End 0 chr1 1687105 1687115 1 chr1 1687115 1687125 2 chr1 1687125 1687135 3 chr1 1687135 1687145 4 chr1 1687145 1687155 5 chr1 1687155 1687165 6 chr1 1687165 1687171 bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpat1wc0el/f1.bed) bedtools_df Chromosome Start End 0 chr1 748225 748235 1 chr1 748235 748245 2 chr1 748245 748255 3 chr1 748255 748265 4 chr1 748265 748275 ... ... ... ... 8443 chr3 8301518 8301528 8444 chr3 8301528 8301538 8445 chr3 8301538 8301548 8446 chr3 8301548 8301558 8447 chr3 8301558 8301568 [8448 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpjcxdvd09/f1.bed) bedtools_df Chromosome Start End 0 chr1 6486431 6486441 1 chr1 6486441 6486451 2 chr1 6486451 6486461 3 chr1 6486461 6486471 4 chr1 6486471 6486481 ... ... ... ... 1426 chr22 6493831 6493841 1427 chr22 6493841 6493851 1428 chr22 6493851 6493861 1429 chr22 6493861 6493871 1430 chr22 6493871 6493881 [1431 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpy3ncwqa2/f1.bed) bedtools_df Chromosome Start End 0 chr18 3391815 3391825 1 chr18 3391825 3391835 2 chr18 3391835 3391845 3 chr18 3391845 3391855 4 chr18 3391855 3391865 .. ... ... ... 668 chr18 3398495 3398505 669 chr18 3398505 3398515 670 chr18 3398515 3398525 671 chr18 3398525 3398535 672 chr18 3398535 3398537 [673 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpi57n1e45/f1.bed) bedtools_df Chromosome Start End 0 chr1 2063061 2063071 1 chr1 2063071 2063081 2 chr1 2063081 2063091 3 chr1 2063091 2063101 4 chr1 2063101 2063111 ... ... ... ... 8919 chr18 3564650 3564660 8920 chr18 3564660 3564670 8921 chr18 3564670 3564680 8922 chr18 3564680 3564690 8923 chr18 3564690 3564691 [8924 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpwq3ozbyh/f1.bed) bedtools_df Chromosome Start End 0 chr1 1724372 1724382 1 chr1 1724382 1724392 2 chr1 1724392 1724402 3 chr1 1724402 1724412 4 chr1 1724412 1724422 ... ... ... ... 5495 chr6 1734322 1734332 5496 chr6 1734332 1734342 5497 chr6 1734342 1734352 5498 chr6 1734352 1734362 5499 chr6 1734362 1734372 [5500 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp0wrfc8sy/f1.bed) bedtools_df Chromosome Start End 0 chr1 4083349 4083359 1 chr1 4083359 4083369 2 chr1 4083369 4083379 3 chr1 4083379 4083389 4 chr1 4083389 4083399 .. ... ... ... 212 chr1 4085469 4085479 213 chr1 4085479 4085489 214 chr1 4085489 4085499 215 chr1 4085499 4085509 216 chr1 4085509 4085517 [217 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpb6dkw82m/f1.bed) bedtools_df Chromosome Start End 0 chr1 561112 561122 1 chr1 561122 561132 2 chr1 561132 561142 3 chr1 561142 561152 4 chr1 561152 561162 ... ... ... ... 5045 chr21 5583596 5583606 5046 chr21 5583606 5583616 5047 chr21 5583616 5583626 5048 chr21 5583626 5583629 5049 chr5 5918556 5918557 [5050 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp81c3zs92/f1.bed) bedtools_df Chromosome Start End 0 chr1 3616957 3616967 1 chr1 3616967 3616977 2 chr1 3616977 3616987 3 chr1 3616987 3616997 4 chr1 3616997 3617007 .. ... ... ... 799 chr1 3624947 3624957 800 chr1 3624957 3624967 801 chr1 3624967 3624977 802 chr1 3624977 3624987 803 chr1 3624987 3624992 [804 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpc3utw5ww/f1.bed) bedtools_df Chromosome Start End 0 chr1 2738863 2738873 1 chr1 2738873 2738883 2 chr1 2738883 2738893 3 chr1 2738893 2738903 4 chr1 2738903 2738913 ... ... ... ... 2954 chr4 9992057 9992067 2955 chr4 9992067 9992077 2956 chr4 9992077 9992087 2957 chr4 9992087 9992097 2958 chr4 9992097 9992107 [2959 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpyer775pr/f1.bed) bedtools_df Chromosome Start End 0 chr1 4421313 4421323 1 chr1 4421323 4421333 2 chr1 4421333 4421343 3 chr1 4421343 4421353 4 chr1 4421353 4421363 ... ... ... ... 4224 chrM 6783858 6783868 4225 chrM 6783868 6783878 4226 chrM 6783878 6783888 4227 chrM 6783888 6783898 4228 chrM 6783898 6783902 [4229 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpra65icwl/f1.bed) bedtools_df Chromosome Start End 0 chr1 3244477 3244487 1 chr1 3244487 3244497 2 chr1 3244497 3244507 3 chr1 3244507 3244517 4 chr1 3244517 3244527 ... ... ... ... 5678 chrM 724995 725005 5679 chrM 725005 725015 5680 chrM 725015 725025 5681 chrM 725025 725035 5682 chrM 725035 725041 [5683 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpk2rnkngn/f1.bed) bedtools_df Chromosome Start End 0 chr1 3962055 3962065 1 chr1 3962065 3962075 2 chr1 3962075 3962085 3 chr1 3962085 3962095 4 chr1 3962095 3962105 ... ... ... ... 2734 chrY 5634016 5634026 2735 chrY 5634026 5634036 2736 chrY 5634036 5634046 2737 chrY 5634046 5634056 2738 chrY 5634056 5634061 [2739 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpfa819zh0/f1.bed) bedtools_df Chromosome Start End 0 chr14 3672823 3672833 1 chr14 3672833 3672843 2 chr14 3672843 3672853 3 chr14 3672853 3672863 4 chr14 3672863 3672873 .. ... ... ... 903 chr14 3681853 3681863 904 chr14 3681863 3681873 905 chr14 3681873 3681883 906 chr14 3681883 3681893 907 chr14 3681893 3681903 [908 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpdvsl1l4j/f1.bed) bedtools_df Chromosome Start End 0 chr1 1 11 1 chr1 11 21 2 chr1 21 31 3 chr1 31 41 4 chr1 41 51 ... ... ... ... 5171 chr2 7385925 7385935 5172 chr2 7385935 7385945 5173 chr2 7385945 7385955 5174 chr2 7385955 7385965 5175 chr2 7385965 7385971 [5176 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpl1iji0_j/f1.bed) bedtools_df Chromosome Start End 0 chr1 9455827 9455837 1 chr1 9455837 9455847 2 chr1 9455847 9455857 3 chr1 9455857 9455867 4 chr1 9455867 9455877 ... ... ... ... 1606 chrM 1504240 1504250 1607 chrM 1504250 1504260 1608 chrM 1504260 1504270 1609 chrM 1504270 1504280 1610 chrM 1504280 1504285 [1611 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpfjm8lavf/f1.bed) bedtools_df Chromosome Start End 0 chr1 6819875 6819885 1 chr1 6819885 6819895 2 chr1 6819895 6819905 3 chr1 6819905 6819915 4 chr1 6819915 6819925 ... ... ... ... 1960 chrX 424505 424515 1961 chrX 424515 424525 1962 chrX 424525 424535 1963 chrX 424535 424545 1964 chrX 424545 424551 [1965 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpm2qpaanw/f1.bed) bedtools_df Chromosome Start End 0 chr1 2091328 2091338 1 chr1 2091338 2091348 2 chr1 2091348 2091358 3 chr1 2091358 2091368 4 chr1 2091368 2091378 ... ... ... ... 1517 chr15 1840464 1840474 1518 chr15 1840474 1840484 1519 chr15 1840484 1840494 1520 chr15 1840494 1840504 1521 chr15 1840504 1840513 [1522 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpttoy2zvu/f1.bed) bedtools_df Chromosome Start End 0 chr1 1 11 1 chr1 11 21 2 chr1 21 31 3 chr1 31 41 4 chr1 41 51 ... ... ... ... 3883 chr5 8606537 8606547 3884 chr5 8606547 8606557 3885 chr5 8606557 8606567 3886 chr5 8606567 8606577 3887 chr5 8606577 8606582 [3888 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpjfb2igkn/f1.bed) bedtools_df Chromosome Start End 0 chr10 5361786 5361796 1 chr10 5361796 5361806 2 chr10 5361806 5361816 3 chr10 5361816 5361826 4 chr10 5361826 5361836 .. ... ... ... 784 chr10 5369626 5369636 785 chr10 5369636 5369646 786 chr10 5369646 5369656 787 chr10 5369656 5369666 788 chr10 5369666 5369669 [789 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpzacubw25/f1.bed) bedtools_df Chromosome Start End 0 chr1 5254556 5254566 1 chr1 5254566 5254576 2 chr1 5254576 5254586 3 chr1 5254586 5254596 4 chr1 5254596 5254606 .. ... ... ... 474 chr1 5259296 5259306 475 chr1 5259306 5259316 476 chr1 5259316 5259326 477 chr1 5259326 5259336 478 chr1 5259336 5259337 [479 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp_bpns0hj/f1.bed) bedtools_df Chromosome Start End 0 chr1 5706315 5706325 1 chr1 5706325 5706335 2 chr1 5706335 5706345 3 chr1 5706345 5706355 4 chr1 5706355 5706365 ... ... ... ... 1055 chr1 7132303 7132313 1056 chr1 7132313 7132323 1057 chr1 7132323 7132333 1058 chr1 7132333 7132343 1059 chr1 7132343 7132350 [1060 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp4jxlynx5/f1.bed) bedtools_df Chromosome Start End 0 chr1 1477083 1477093 1 chr1 1477093 1477103 2 chr1 1477103 1477113 3 chr1 1477113 1477123 4 chr1 1477123 1477133 ... ... ... ... 2774 chr1 5791419 5791429 2775 chr1 5791429 5791439 2776 chr1 5791439 5791449 2777 chr1 5791449 5791459 2778 chr1 5791459 5791463 [2779 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp_gifydyd/f1.bed) bedtools_df Chromosome Start End 0 chr1 4127325 4127335 1 chr1 4127335 4127345 2 chr1 4127345 4127355 3 chr1 4127355 4127365 4 chr1 4127365 4127375 ... ... ... ... 1346 chrX 3034420 3034430 1347 chrX 3034430 3034440 1348 chrX 3034440 3034450 1349 chrX 3034450 3034460 1350 chrX 3034460 3034466 [1351 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpi0rjdhh_/f1.bed) bedtools_df Chromosome Start End 0 chr1 1186987 1186997 1 chr1 1186997 1187007 2 chr1 1187007 1187017 3 chr1 1187017 1187027 4 chr1 1187027 1187037 ... ... ... ... 4466 chr8 8851028 8851038 4467 chr8 8851038 8851048 4468 chr8 8851048 8851058 4469 chr8 8851058 8851068 4470 chr8 8851068 8851076 [4471 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp7hqq8hyv/f1.bed) bedtools_df Chromosome Start End 0 chr1 410476 410486 1 chr1 410486 410496 2 chr1 410496 410506 3 chr1 410506 410516 4 chr1 410516 410526 ... ... ... ... 7365 chr21 10001579 10001589 7366 chr21 10001589 10001599 7367 chr21 10001599 10001609 7368 chr21 10001609 10001619 7369 chr21 10001619 10001625 [7370 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpa4zhge24/f1.bed) bedtools_df Chromosome Start End 0 chr1 483399 483409 1 chr1 483409 483419 2 chr1 483419 483429 3 chr1 483429 483439 4 chr1 483439 483449 ... ... ... ... 5889 chr6 10006370 10006380 5890 chr6 10006380 10006390 5891 chr6 10006390 10006400 5892 chr6 10006400 10006410 5893 chr6 10006410 10006419 [5894 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpsze61k23/f1.bed) bedtools_df Chromosome Start End 0 chr1 4669756 4669766 1 chr1 4669766 4669776 2 chr1 4669776 4669786 3 chr1 4669786 4669796 4 chr1 4669796 4669806 ... ... ... ... 1905 chr18 8794425 8794435 1906 chr18 8794435 8794445 1907 chr18 8794445 8794455 1908 chr18 8794455 8794465 1909 chr18 8794465 8794471 [1910 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpilwfdbrd/f1.bed) bedtools_df Chromosome Start End 0 chr2 2138662 2138672 1 chr2 2138672 2138682 2 chr2 2138682 2138692 3 chr2 2138692 2138702 4 chr2 2138702 2138712 ... ... ... ... 1432 chr9 2145872 2145882 1433 chr9 2145882 2145892 1434 chr9 2145892 2145902 1435 chr9 2145902 2145912 1436 chr9 2145912 2145915 [1437 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp97lqpmkv/f1.bed) bedtools_df Chromosome Start End 0 chr1 2935139 2935149 1 chr1 2935149 2935159 2 chr1 2935159 2935169 3 chr1 2935169 2935179 4 chr1 2935179 2935189 ... ... ... ... 1647 chr12 2941999 2942009 1648 chr12 2942009 2942019 1649 chr12 2942019 2942029 1650 chr12 2942029 2942039 1651 chr12 2942039 2942049 [1652 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpv0rbmhlm/f1.bed) bedtools_df Chromosome Start End 0 chr1 100775 100785 1 chr1 100785 100795 2 chr1 100795 100805 3 chr1 100805 100815 4 chr1 100815 100825 ... ... ... ... 5886 chrX 8742741 8742751 5887 chrX 8742751 8742761 5888 chrX 8742761 8742771 5889 chrX 8742771 8742781 5890 chrX 8742781 8742786 [5891 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp8dfcwinu/f1.bed) bedtools_df Chromosome Start End 0 chr1 1618930 1618940 1 chr1 1618940 1618950 2 chr1 1618950 1618960 3 chr1 1618960 1618970 4 chr1 1618970 1618980 .. ... ... ... 964 chr21 3051341 3051351 965 chr21 3051351 3051361 966 chr21 3051361 3051371 967 chr21 3051371 3051381 968 chr21 3051381 3051383 [969 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpu8q6tob7/f1.bed) bedtools_df Chromosome Start End 0 chr1 8935410 8935420 1 chr1 8935420 8935430 2 chr1 8935430 8935440 3 chr1 8935440 8935450 4 chr1 8935450 8935460 ... ... ... ... 1238 chr4 8254847 8254857 1239 chr4 8254857 8254867 1240 chr4 8254867 8254877 1241 chr4 8254877 8254887 1242 chr4 8254887 8254888 [1243 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpha9lax5_/f1.bed) bedtools_df Chromosome Start End 0 chr1 1025644 1025654 1 chr1 1025654 1025664 2 chr1 1025664 1025674 3 chr1 1025674 1025684 4 chr1 1025684 1025694 ... ... ... ... 1445 chrM 4492293 4492303 1446 chrM 4492303 4492313 1447 chrM 4492313 4492323 1448 chrM 4492323 4492333 1449 chrM 4492333 4492336 [1450 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpltn30jmd/f1.bed) bedtools_df Chromosome Start End 0 chr1 5313454 5313464 1 chr1 5313464 5313474 2 chr1 5313474 5313484 3 chr1 5313484 5313494 4 chr1 5313494 5313504 ... ... ... ... 1126 chrM 4374473 4374483 1127 chrM 4374483 4374493 1128 chrM 4374493 4374503 1129 chrM 4374503 4374513 1130 chrM 4374513 4374517 [1131 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpoi1bwlsd/f1.bed) bedtools_df Chromosome Start End 0 chr1 2 12 1 chr1 12 22 2 chr1 22 32 3 chr1 32 42 4 chr1 42 52 ... ... ... ... 3219 chrM 5397972 5397982 3220 chrM 5397982 5397992 3221 chrM 5397992 5398002 3222 chrM 5398002 5398012 3223 chrM 5398012 5398016 [3224 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp7lp89xo6/f1.bed) bedtools_df Chromosome Start End 0 chr1 1810201 1810211 1 chr1 1810211 1810221 2 chr1 1810221 1810231 3 chr1 1810231 1810241 4 chr1 1810241 1810251 ... ... ... ... 2870 chr14 5234076 5234086 2871 chr14 5234086 5234096 2872 chr14 5234096 5234106 2873 chr14 5234106 5234116 2874 chr14 5234116 5234118 [2875 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp2ia5tzn_/f1.bed) bedtools_df Chromosome Start End 0 chr1 630669 630679 1 chr1 630679 630689 2 chr1 630689 630699 3 chr1 630699 630709 4 chr1 630709 630719 ... ... ... ... 6166 chr1 8579575 8579585 6167 chr1 8579585 8579595 6168 chr1 8579595 8579605 6169 chr1 8579605 8579615 6170 chr1 8579615 8579620 [6171 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp4pjof2hm/f1.bed) bedtools_df Chromosome Start End 0 chr1 5263555 5263556 1 chr1 5263555 5263565 2 chr1 5263565 5263575 3 chr1 5263575 5263585 4 chr1 5263585 5263595 ... ... ... ... 5764 chr22 5273005 5273015 5765 chr22 5273015 5273025 5766 chr22 5273025 5273035 5767 chr22 5273035 5273045 5768 chr22 5273045 5273052 [5769 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpguo4spfj/f1.bed) bedtools_df Chromosome Start End 0 chr1 613070 613080 1 chr1 613080 613090 2 chr1 613090 613100 3 chr1 613100 613110 4 chr1 613110 613120 .. ... ... ... 964 chr1 6170975 6170985 965 chr1 6170985 6170995 966 chr1 6170995 6171005 967 chr1 6171005 6171015 968 chr1 6171015 6171016 [969 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpxp781fzk/f1.bed) bedtools_df Chromosome Start End 0 chr1 2377477 2377487 1 chr1 2377487 2377497 2 chr1 2377497 2377507 3 chr1 2377507 2377517 4 chr1 2377517 2377527 ... ... ... ... 5751 chrM 9937606 9937616 5752 chrM 9937616 9937626 5753 chrM 9937626 9937636 5754 chrM 9937636 9937646 5755 chrM 9937646 9937650 [5756 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpj_oml_8w/f1.bed) bedtools_df Chromosome Start End 0 chr1 3823526 3823536 1 chr1 3823536 3823546 2 chr1 3823546 3823556 3 chr1 3823556 3823566 4 chr1 3823566 3823576 ... ... ... ... 2458 chr1 9820816 9820826 2459 chr1 9820826 9820836 2460 chr1 9820836 9820846 2461 chr1 9820846 9820856 2462 chr1 9820856 9820857 [2463 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp_c8cb9b_/f1.bed) bedtools_df Chromosome Start End 0 chr1 2 12 1 chr1 12 22 2 chr1 22 32 3 chr1 32 42 4 chr1 42 52 ... ... ... ... 5563 chr7 6879894 6879904 5564 chr7 6879904 6879914 5565 chr7 6879914 6879924 5566 chr7 6879924 6879934 5567 chr7 6879934 6879937 [5568 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpl8993q74/f1.bed) bedtools_df Chromosome Start End 0 chr1 5681537 5681547 1 chr1 5681547 5681557 2 chr1 5681557 5681567 3 chr1 5681567 5681577 4 chr1 5681577 5681587 .. ... ... ... 460 chr1 5686137 5686147 461 chr1 5686147 5686157 462 chr1 5686157 5686167 463 chr1 5686167 5686177 464 chr1 5686177 5686181 [465 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpna22ljyx/f1.bed) bedtools_df Chromosome Start End 0 chr1 5215059 5215060 1 chr1 8266070 8266080 2 chr1 8266080 8266090 3 chr1 8266090 8266100 4 chr1 8266100 8266110 ... ... ... ... 1474 chr6 3195832 3195842 1475 chr6 3195842 3195852 1476 chr6 3195852 3195862 1477 chr6 3195862 3195872 1478 chr6 3195872 3195878 [1479 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpututsjel/f1.bed) bedtools_df Chromosome Start End 0 chr1 3017420 3017430 1 chr1 3017430 3017440 2 chr1 3017440 3017450 3 chr1 3017450 3017460 4 chr1 3017460 3017470 ... ... ... ... 2732 chr18 9681367 9681377 2733 chr18 9681377 9681386 2734 chr9 8857229 8857239 2735 chr9 8857239 8857249 2736 chr9 8857249 8857257 [2737 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpwcimwgzf/f1.bed) bedtools_df Chromosome Start End 0 chr1 553585 553595 1 chr1 553595 553605 2 chr1 553605 553615 3 chr1 553615 553625 4 chr1 553625 553635 ... ... ... ... 2939 chr3 803947 803957 2940 chr3 803957 803967 2941 chr3 803967 803977 2942 chr3 803977 803987 2943 chr3 803987 803989 [2944 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpfmjoci5h/f1.bed) bedtools_df Chromosome Start End 0 chr1 2191971 2191981 1 chr1 2191981 2191991 2 chr1 2191991 2192001 3 chr1 2192001 2192011 4 chr1 2192011 2192021 ... ... ... ... 3227 chr19 9769949 9769959 3228 chr19 9769959 9769969 3229 chr19 9769969 9769979 3230 chr19 9769979 9769989 3231 chr19 9769989 9769999 [3232 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpcgqvb5fx/f1.bed) bedtools_df Chromosome Start End 0 chr1 4915425 4915435 1 chr1 4915435 4915445 2 chr1 4915445 4915455 3 chr1 4915455 4915465 4 chr1 4915465 4915475 ... ... ... ... 4269 chr22 4921405 4921415 4270 chr22 4921415 4921425 4271 chr22 4921425 4921435 4272 chr22 4921435 4921445 4273 chr22 4921445 4921455 [4274 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpfre2580g/f1.bed) bedtools_df Chromosome Start End 0 chr1 1896141 1896151 1 chr1 1896151 1896161 2 chr1 1896161 1896171 3 chr1 1896171 1896181 4 chr1 1896181 1896191 ... ... ... ... 3110 chrX 8656708 8656718 3111 chrX 8656718 8656728 3112 chrX 8656728 8656738 3113 chrX 8656738 8656748 3114 chrX 8656748 8656756 [3115 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpwnv54tfp/f1.bed) bedtools_df Chromosome Start End 0 chr2 731735 731745 1 chr2 731745 731755 2 chr2 731755 731765 3 chr2 731765 731775 4 chr2 731775 731785 .. ... ... ... 582 chr2 737555 737565 583 chr2 737565 737575 584 chr2 737575 737585 585 chr2 737585 737595 586 chr2 737595 737598 [587 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpre415oe3/f1.bed) bedtools_df Chromosome Start End 0 chr14 1237721 1237731 1 chr14 1237731 1237741 2 chr14 1237741 1237751 3 chr14 1237751 1237761 4 chr14 1237761 1237771 ... ... ... ... 2308 chrX 278019 278029 2309 chrX 278029 278039 2310 chrX 278039 278049 2311 chrX 278049 278059 2312 chrX 278059 278062 [2313 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpxc7vxtqx/f1.bed) bedtools_df Chromosome Start End 0 chr1 5898365 5898375 1 chr1 5898375 5898385 2 chr1 5898385 5898395 3 chr1 5898395 5898405 4 chr1 5898405 5898415 5 chr1 5898415 5898425 6 chr1 5898425 5898435 7 chr1 5898435 5898445 8 chr1 5898445 5898455 9 chr1 5898455 5898465 10 chr1 5898465 5898475 11 chr1 5898475 5898485 12 chr1 5898485 5898495 13 chr1 5898495 5898505 14 chr1 5898505 5898515 15 chr1 5898515 5898525 16 chr1 5898525 5898535 17 chr1 5898535 5898545 18 chr1 5898545 5898555 19 chr1 5898555 5898565 20 chr1 5898565 5898575 21 chr1 5898575 5898585 22 chr1 5898585 5898590 bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp3qrx64d_/f1.bed) bedtools_df Chromosome Start End 0 chr1 1 2 __________ test_three_in_a_row[strandedness_chain435-method_chain435] __________ [gw1] linux -- Python 3.12.6 /usr/bin/python3.12 strandedness_chain = ('opposite', None) method_chain = ('join', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('join', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/getitem.py:15 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:145 E (and 24 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2BAAEYUCgwAAD4AAw==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') _____________________________ test_cluster[False] ______________________________ [gw9] linux -- Python 3.12.6 /usr/bin/python3.12 strand = False @pytest.mark.bedtools > @pytest.mark.parametrize("strand", [True, False]) tests/test_unary.py:96: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_unary.py:132: in test_cluster result = gr.cluster(strand=strand) pyranges/pyranges.py:1070: in cluster df = pyrange_apply_single(_cluster, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/cluster.py:14: in _cluster ids = annotate_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_cluster( E strand=False, E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., # or any other generated value E ) sorted_nearest/src/annotate_clusters.pyx:15: Exception ----------------------------- Captured stdout call ----------------------------- +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpa6k9z8a7/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 2 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6188695 | 6197657 | a | 0 | + | | chr1 | 6188695 | 6194721 | a | 0 | + | | chr1 | 6188695 | 6197028 | a | 0 | - | | chr18 | 6188695 | 6188696 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chrX | 6188695 | 6196588 | a | 0 | + | | chrX | 6188695 | 6197320 | a | 0 | + | | chrX | 6188695 | 6198295 | a | 0 | + | | chrX | 6188695 | 6192896 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp5sw1jzxd/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 6188695 6194721 a 0 + 1 1 chr1 6188695 6197028 a 0 - 1 2 chr1 6188695 6197657 a 0 + 1 3 chr18 6188695 6188696 a 0 + 2 4 chr21 6188695 6190062 a 0 + 3 5 chrX 6188695 6192896 a 0 + 4 6 chrX 6188695 6194565 a 0 + 4 7 chrX 6188695 6196484 a 0 + 4 8 chrX 6188695 6196588 a 0 + 4 9 chrX 6188695 6197320 a 0 + 4 10 chrX 6188695 6198295 a 0 + 4 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6188695 | 6197657 | a | 0 | + | | chr1 | 6188695 | 6194721 | a | 0 | + | | chr1 | 6188695 | 6197028 | a | 0 | - | | chr18 | 6188695 | 6188696 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chrX | 6188695 | 6196588 | a | 0 | + | | chrX | 6188695 | 6197320 | a | 0 | + | | chrX | 6188695 | 6198295 | a | 0 | + | | chrX | 6188695 | 6192896 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6188695 | 6194565 | a | 0 | + | | chr1 | 6188695 | 6197657 | a | 0 | + | | chr1 | 6188695 | 6188952 | a | 0 | + | | chr18 | 6188695 | 6188696 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chrX | 6188695 | 6196588 | a | 0 | + | | chrX | 6188695 | 6197320 | a | 0 | + | | chrX | 6188695 | 6192896 | a | 0 | + | | chrX | 6188695 | 6198295 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 10 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpobdp5fnz/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 6188695 6188952 a 0 + 1 1 chr1 6188695 6194565 a 0 + 1 2 chr1 6188695 6197657 a 0 + 1 3 chr18 6188695 6188696 a 0 + 2 4 chr21 6188695 6190062 a 0 + 3 5 chrX 6188695 6192896 a 0 + 4 6 chrX 6188695 6196484 a 0 + 4 7 chrX 6188695 6196588 a 0 + 4 8 chrX 6188695 6197320 a 0 + 4 9 chrX 6188695 6198295 a 0 - 4 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6188695 | 6194565 | a | 0 | + | | chr1 | 6188695 | 6197657 | a | 0 | + | | chr1 | 6188695 | 6188952 | a | 0 | + | | chr18 | 6188695 | 6188696 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chrX | 6188695 | 6196588 | a | 0 | + | | chrX | 6188695 | 6197320 | a | 0 | + | | chrX | 6188695 | 6192896 | a | 0 | + | | chrX | 6188695 | 6198295 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 10 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7 | 264 | a | 0 | + | | chr1 | 8 | 9 | a | 0 | + | | chr1 | 7893 | 7894 | a | 0 | + | | chr1 | 2 | 3 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr1 | 3 | 4 | a | 0 | + | | chr1 | 65537 | 65538 | a | 0 | + | | chr1 | 65537 | 65538 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 9 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp579b0mqu/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 2 a 0 - 1 1 chr1 2 3 a 0 + 1 2 chr1 3 4 a 0 + 1 3 chr1 7 264 a 0 + 2 4 chr1 8 9 a 0 + 2 5 chr1 7893 7894 a 0 + 3 6 chr1 65537 65538 a 0 + 4 7 chr1 65537 65538 a 0 + 4 8 chr18 6 7 a 0 + 5 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7 | 264 | a | 0 | + | | chr1 | 8 | 9 | a | 0 | + | | chr1 | 7893 | 7894 | a | 0 | + | | chr1 | 2 | 3 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr1 | 3 | 4 | a | 0 | + | | chr1 | 65537 | 65538 | a | 0 | + | | chr1 | 65537 | 65538 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 9 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7 | 264 | a | 0 | + | | chr1 | 8 | 9 | a | 0 | + | | chr1 | 7893 | 7894 | a | 0 | + | | chr1 | 2 | 3 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr1 | 3 | 4 | a | 0 | + | | chr1 | 65537 | 65538 | a | 0 | + | | chr1 | 65537 | 65538 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 9 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpzjzvf3t_/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 2 a 0 - 1 1 chr1 2 3 a 0 + 1 2 chr1 3 4 a 0 + 1 3 chr1 7 264 a 0 + 2 4 chr1 8 9 a 0 + 2 5 chr1 7893 7894 a 0 + 3 6 chr1 65537 65538 a 0 + 4 7 chr1 65537 65538 a 0 + 4 8 chr18 6 7 a 0 + 5 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7 | 264 | a | 0 | + | | chr1 | 8 | 9 | a | 0 | + | | chr1 | 7893 | 7894 | a | 0 | + | | chr1 | 2 | 3 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr1 | 3 | 4 | a | 0 | + | | chr1 | 65537 | 65538 | a | 0 | + | | chr1 | 65537 | 65538 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 9 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | | chr1 | 7 | 264 | a | 0 | + | | chr1 | 8 | 9 | a | 0 | + | | chr1 | 7893 | 7894 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr1 | 2 | 3 | a | 0 | + | | chr1 | 3 | 4 | a | 0 | + | | chr1 | 65537 | 65538 | a | 0 | + | | chr1 | 65537 | 65538 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 9 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp0z70p5y1/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 2 a 0 + 1 1 chr1 2 3 a 0 + 1 2 chr1 3 4 a 0 + 1 3 chr1 7 264 a 0 + 2 4 chr1 8 9 a 0 + 2 5 chr1 7893 7894 a 0 + 3 6 chr1 65537 65538 a 0 + 4 7 chr1 65537 65538 a 0 + 4 8 chr18 6 7 a 0 + 5 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | | chr1 | 7 | 264 | a | 0 | + | | chr1 | 8 | 9 | a | 0 | + | | chr1 | 7893 | 7894 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr1 | 2 | 3 | a | 0 | + | | chr1 | 3 | 4 | a | 0 | + | | chr1 | 65537 | 65538 | a | 0 | + | | chr1 | 65537 | 65538 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 9 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | | chr1 | 7 | 264 | a | 0 | + | | chr1 | 8 | 9 | a | 0 | + | | chr1 | 7893 | 7894 | a | 0 | + | | chr1 | 2 | 3 | a | 0 | + | | chr1 | 3 | 4 | a | 0 | + | | chr1 | 65537 | 65538 | a | 0 | + | | chr18 | 6 | 7 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 8 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpa2klrc89/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 2 a 0 + 1 1 chr1 2 3 a 0 + 1 2 chr1 3 4 a 0 + 1 3 chr1 7 264 a 0 + 2 4 chr1 8 9 a 0 + 2 5 chr1 7893 7894 a 0 + 3 6 chr1 65537 65538 a 0 + 4 7 chr18 6 7 a 0 + 5 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | | chr1 | 7 | 264 | a | 0 | + | | chr1 | 8 | 9 | a | 0 | + | | chr1 | 7893 | 7894 | a | 0 | + | | chr1 | 2 | 3 | a | 0 | + | | chr1 | 3 | 4 | a | 0 | + | | chr1 | 65537 | 65538 | a | 0 | + | | chr18 | 6 | 7 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 8 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5 | 9 | a | 0 | + | | chr1 | 65537 | 65543 | a | 0 | + | | chr1 | 5 | 6 | a | 0 | + | | chr1 | 5 | 11 | a | 0 | + | | chr1 | 5 | 11 | a | 0 | + | | chr1 | 5 | 10 | a | 0 | + | | chr1 | 5 | 7 | a | 0 | + | | chr1 | 5 | 262 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 8 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp820cdijm/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 5 10 a 0 + 1 1 chr1 5 11 a 0 + 1 2 chr1 5 11 a 0 + 1 3 chr1 5 262 a 0 + 1 4 chr1 5 6 a 0 + 1 5 chr1 5 7 a 0 + 1 6 chr1 5 9 a 0 + 1 7 chr1 65537 65543 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5 | 9 | a | 0 | + | | chr1 | 65537 | 65543 | a | 0 | + | | chr1 | 5 | 6 | a | 0 | + | | chr1 | 5 | 11 | a | 0 | + | | chr1 | 5 | 11 | a | 0 | + | | chr1 | 5 | 10 | a | 0 | + | | chr1 | 5 | 7 | a | 0 | + | | chr1 | 5 | 262 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 8 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5661021 | 5668175 | a | 0 | - | | chr1 | 5661021 | 5668175 | a | 0 | - | | chr1 | 530563 | 537717 | a | 0 | - | | chr1 | 5661021 | 5668175 | a | 0 | - | | chr1 | 5661021 | 5662517 | a | 0 | - | | chr20 | 5661021 | 5668175 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmptxcypv4v/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 530563 537717 a 0 - 1 1 chr1 5661021 5662517 a 0 - 2 2 chr1 5661021 5668175 a 0 - 2 3 chr1 5661021 5668175 a 0 - 2 4 chr1 5661021 5668175 a 0 - 2 5 chr20 5661021 5668175 a 0 + 3 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5661021 | 5668175 | a | 0 | - | | chr1 | 5661021 | 5668175 | a | 0 | - | | chr1 | 530563 | 537717 | a | 0 | - | | chr1 | 5661021 | 5668175 | a | 0 | - | | chr1 | 5661021 | 5662517 | a | 0 | - | | chr20 | 5661021 | 5668175 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5661021 | 5666751 | a | 0 | - | | chr1 | 5661021 | 5666751 | a | 0 | - | | chr1 | 530563 | 532636 | a | 0 | - | | chr1 | 5661021 | 5666751 | a | 0 | - | | chr1 | 5661021 | 5666751 | a | 0 | - | | chr20 | 5661021 | 5666751 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp42ksu__0/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 530563 532636 a 0 - 1 1 chr1 5661021 5666751 a 0 - 2 2 chr1 5661021 5666751 a 0 - 2 3 chr1 5661021 5666751 a 0 - 2 4 chr1 5661021 5666751 a 0 - 2 5 chr20 5661021 5666751 a 0 + 3 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5661021 | 5666751 | a | 0 | - | | chr1 | 5661021 | 5666751 | a | 0 | - | | chr1 | 530563 | 532636 | a | 0 | - | | chr1 | 5661021 | 5666751 | a | 0 | - | | chr1 | 5661021 | 5666751 | a | 0 | - | | chr20 | 5661021 | 5666751 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp_o1z4ve5/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 2 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpu8gwy0n6/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 2 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpmx1rokhe/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 2 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpv9ayzhda/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 2 a 0 - 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpyjd06p_x/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 2 a 0 - 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9127045 | 9133566 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmppam0i6s1/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 9127045 9133566 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9127045 | 9133566 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 908919 | 913877 | a | 0 | - | | chr1 | 3604163 | 3611726 | a | 0 | - | | chr1 | 2508911 | 2516294 | a | 0 | - | | chr1 | 9818873 | 9825443 | a | 0 | - | | chr6 | 4348224 | 4352096 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpu1ue_wz5/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 908919 913877 a 0 - 1 1 chr1 2508911 2516294 a 0 - 2 2 chr1 3604163 3611726 a 0 - 3 3 chr1 9818873 9825443 a 0 - 4 4 chr6 4348224 4352096 a 0 - 5 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 908919 | 913877 | a | 0 | - | | chr1 | 3604163 | 3611726 | a | 0 | - | | chr1 | 2508911 | 2516294 | a | 0 | - | | chr1 | 9818873 | 9825443 | a | 0 | - | | chr6 | 4348224 | 4352096 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2946866 | 2955787 | a | 0 | - | | chrY | 4930797 | 4931158 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp12d7ak5e/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2946866 2955787 a 0 - 1 1 chrY 4930797 4931158 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2946866 | 2955787 | a | 0 | - | | chrY | 4930797 | 4931158 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 591412 | 599477 | a | 0 | + | | chr1 | 1658436 | 1661274 | a | 0 | + | | chr1 | 4588716 | 4590866 | a | 0 | - | | chr18 | 2115439 | 2118085 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp3yh3y_co/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 591412 599477 a 0 + 1 1 chr1 1658436 1661274 a 0 + 2 2 chr1 4588716 4590866 a 0 - 3 3 chr18 2115439 2118085 a 0 + 4 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 591412 | 599477 | a | 0 | + | | chr1 | 1658436 | 1661274 | a | 0 | + | | chr1 | 4588716 | 4590866 | a | 0 | - | | chr18 | 2115439 | 2118085 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr8 | 1579013 | 1579622 | a | 0 | + | | chr8 | 1262024 | 1271533 | a | 0 | - | | chr11 | 4290868 | 4294032 | a | 0 | + | | chr19 | 4892906 | 4896107 | a | 0 | + | | chr19 | 6117392 | 6124581 | a | 0 | - | | chr21 | 4583646 | 4589591 | a | 0 | - | | chrY | 1558469 | 1559593 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 7 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp2a0_8y3i/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr11 4290868 4294032 a 0 + 1 1 chr19 4892906 4896107 a 0 + 2 2 chr19 6117392 6124581 a 0 - 3 3 chr21 4583646 4589591 a 0 - 4 4 chr8 1262024 1271533 a 0 - 5 5 chr8 1579013 1579622 a 0 + 6 6 chrY 1558469 1559593 a 0 + 7 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr8 | 1579013 | 1579622 | a | 0 | + | | chr8 | 1262024 | 1271533 | a | 0 | - | | chr11 | 4290868 | 4294032 | a | 0 | + | | chr19 | 4892906 | 4896107 | a | 0 | + | | chr19 | 6117392 | 6124581 | a | 0 | - | | chr21 | 4583646 | 4589591 | a | 0 | - | | chrY | 1558469 | 1559593 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 7 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8966923 | 8967679 | a | 0 | + | | chr1 | 1023661 | 1032063 | a | 0 | + | | chr1 | 4538720 | 4539957 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp09wlq59d/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1023661 1032063 a 0 + 1 1 chr1 4538720 4539957 a 0 - 2 2 chr1 8966923 8967679 a 0 + 3 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8966923 | 8967679 | a | 0 | + | | chr1 | 1023661 | 1032063 | a | 0 | + | | chr1 | 4538720 | 4539957 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2364496 | 2369812 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpd5ijq9n9/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2364496 2369812 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2364496 | 2369812 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2 | 5242 | a | 0 | + | | chr1 | 2 | 9301 | a | 0 | - | | chr1 | 9942545 | 9948120 | a | 0 | - | | chr12 | 2 | 4134 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr15 | 2 | 10001 | a | 0 | + | | chr15 | 2 | 352 | a | 0 | - | | chr15 | 2 | 28 | a | 0 | - | | chr17 | 2 | 3515 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpk4x8fskl/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2 5242 a 0 + 1 1 chr1 2 9301 a 0 - 1 2 chr1 9942545 9948120 a 0 - 2 3 chr12 2 4134 a 0 + 3 4 chr12 8432276 8437564 a 0 - 4 5 chr15 2 10001 a 0 + 5 6 chr15 2 28 a 0 - 5 7 chr15 2 352 a 0 - 5 8 chr17 2 3515 a 0 + 6 9 chr22 2 4077 a 0 - 7 10 chr22 4933616 4933909 a 0 + 8 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2 | 5242 | a | 0 | + | | chr1 | 2 | 9301 | a | 0 | - | | chr1 | 9942545 | 9948120 | a | 0 | - | | chr12 | 2 | 4134 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr15 | 2 | 10001 | a | 0 | + | | chr15 | 2 | 352 | a | 0 | - | | chr15 | 2 | 28 | a | 0 | - | | chr17 | 2 | 3515 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9762037 | 9764366 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpj6sfg4vu/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 9762037 9764366 a 0 - 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9762037 | 9764366 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8785393 | 8785572 | a | 0 | + | | chr1 | 2776909 | 2777088 | a | 0 | + | | chr1 | 9834533 | 9834712 | a | 0 | - | | chr2 | 1385685 | 1385864 | a | 0 | + | | chr12 | 5880555 | 5880734 | a | 0 | + | | chr16 | 3979892 | 3980071 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpyln0uthn/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2776909 2777088 a 0 + 1 1 chr1 8785393 8785572 a 0 + 2 2 chr1 9834533 9834712 a 0 - 3 3 chr12 5880555 5880734 a 0 + 4 4 chr16 3979892 3980071 a 0 - 5 5 chr2 1385685 1385864 a 0 + 6 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8785393 | 8785572 | a | 0 | + | | chr1 | 2776909 | 2777088 | a | 0 | + | | chr1 | 9834533 | 9834712 | a | 0 | - | | chr2 | 1385685 | 1385864 | a | 0 | + | | chr12 | 5880555 | 5880734 | a | 0 | + | | chr16 | 3979892 | 3980071 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7382561 | 7385767 | a | 0 | + | | chr1 | 3818389 | 3820788 | a | 0 | + | | chr1 | 473385 | 475763 | a | 0 | + | | chr1 | 2082919 | 2091757 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr10 | 4594178 | 4597419 | a | 0 | - | | chr13 | 1225183 | 1231212 | a | 0 | + | | chr21 | 4384960 | 4389199 | a | 0 | - | | chrM | 2850859 | 2852507 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 8 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpbtky8qae/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 473385 475763 a 0 + 1 1 chr1 2082919 2091757 a 0 + 2 2 chr1 3818389 3820788 a 0 + 3 3 chr1 7382561 7385767 a 0 + 4 4 chr10 4594178 4597419 a 0 - 5 5 chr13 1225183 1231212 a 0 + 6 6 chr21 4384960 4389199 a 0 - 7 7 chr3 8381129 8390956 a 0 + 8 8 chr5 5660226 5661224 a 0 - 9 9 chr9 8396383 8404423 a 0 - 10 10 chrM 2850859 2852507 a 0 + 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7382561 | 7385767 | a | 0 | + | | chr1 | 3818389 | 3820788 | a | 0 | + | | chr1 | 473385 | 475763 | a | 0 | + | | chr1 | 2082919 | 2091757 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr10 | 4594178 | 4597419 | a | 0 | - | | chr13 | 1225183 | 1231212 | a | 0 | + | | chr21 | 4384960 | 4389199 | a | 0 | - | | chrM | 2850859 | 2852507 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 8 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1911763 | 1913902 | a | 0 | + | | chr1 | 7893159 | 7895298 | a | 0 | + | | chr1 | 2651976 | 2654115 | a | 0 | + | | chr1 | 6821103 | 6825652 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr4 | 8969352 | 8974053 | a | 0 | + | | chr4 | 3160257 | 3162396 | a | 0 | - | | chr4 | 2476951 | 2485870 | a | 0 | - | | chr13 | 3224453 | 3226592 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpuw8tp0tb/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1911763 1913902 a 0 + 1 1 chr1 2651976 2654115 a 0 + 2 2 chr1 5181014 5183153 a 0 - 3 3 chr1 6821103 6825652 a 0 - 4 4 chr1 7893159 7895298 a 0 + 5 5 chr13 3224453 3226592 a 0 + 6 6 chr18 4484864 4490656 a 0 - 7 7 chr3 9674739 9676878 a 0 + 8 8 chr4 2476951 2485870 a 0 - 9 9 chr4 3160257 3162396 a 0 - 10 10 chr4 8969352 8974053 a 0 + 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1911763 | 1913902 | a | 0 | + | | chr1 | 7893159 | 7895298 | a | 0 | + | | chr1 | 2651976 | 2654115 | a | 0 | + | | chr1 | 6821103 | 6825652 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr4 | 8969352 | 8974053 | a | 0 | + | | chr4 | 3160257 | 3162396 | a | 0 | - | | chr4 | 2476951 | 2485870 | a | 0 | - | | chr13 | 3224453 | 3226592 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 10000000 | 10008601 | a | 0 | + | | chr1 | 7843446 | 7849058 | a | 0 | - | | chr1 | 10000000 | 10005532 | a | 0 | - | | chr1 | 6299784 | 6307663 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr18 | 8736472 | 8737791 | a | 0 | - | | chr20 | 2435671 | 2442639 | a | 0 | + | | chr20 | 3239544 | 3242430 | a | 0 | + | | chr21 | 5990565 | 5997045 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 7 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpd7t3x_bz/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 6299784 6307663 a 0 - 1 1 chr1 7843446 7849058 a 0 - 2 2 chr1 10000000 10005532 a 0 - 3 3 chr1 10000000 10008601 a 0 + 3 4 chr12 5812039 5817244 a 0 + 4 5 chr18 8736472 8737791 a 0 - 5 6 chr20 2435671 2442639 a 0 + 6 7 chr20 3239544 3242430 a 0 + 7 8 chr21 5990565 5997045 a 0 + 8 9 chr3 6688209 6693225 a 0 + 9 10 chr8 10000000 10006292 a 0 + 10 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 10000000 | 10008601 | a | 0 | + | | chr1 | 7843446 | 7849058 | a | 0 | - | | chr1 | 10000000 | 10005532 | a | 0 | - | | chr1 | 6299784 | 6307663 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr18 | 8736472 | 8737791 | a | 0 | - | | chr20 | 2435671 | 2442639 | a | 0 | + | | chr20 | 3239544 | 3242430 | a | 0 | + | | chr21 | 5990565 | 5997045 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 7 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr17 | 5890785 | 5894766 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpukmwjiuh/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr17 5890785 5894766 a 0 - 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr17 | 5890785 | 5894766 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3682585 | 3684809 | a | 0 | + | | chr19 | 9510925 | 9518399 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp7d561vmb/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 3682585 3684809 a 0 + 1 1 chr19 9510925 9518399 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3682585 | 3684809 | a | 0 | + | | chr19 | 9510925 | 9518399 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3831079 | 3836124 | a | 0 | + | | chr5 | 9999999 | 10007131 | a | 0 | - | | chr21 | 6779690 | 6789690 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp016ifsb7/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 3831079 3836124 a 0 + 1 1 chr21 6779690 6789690 a 0 - 2 2 chr5 9999999 10007131 a 0 - 3 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3831079 | 3836124 | a | 0 | + | | chr5 | 9999999 | 10007131 | a | 0 | - | | chr21 | 6779690 | 6789690 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4117770 | 4117771 | a | 0 | + | | chr1 | 6346010 | 6346011 | a | 0 | + | | chr1 | 1 | 5511 | a | 0 | + | | chr1 | 7250271 | 7256519 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr3 | 8235258 | 8239581 | a | 0 | - | | chr15 | 4568365 | 4577519 | a | 0 | - | | chr17 | 7054047 | 7060625 | a | 0 | - | | chr19 | 7019821 | 7024212 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp2t_ayiy4/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 5511 a 0 + 1 1 chr1 1315232 1315236 a 0 - 2 2 chr1 1474014 1479792 a 0 - 3 3 chr1 4117770 4117771 a 0 + 4 4 chr1 5281610 5291610 a 0 - 5 5 chr1 6346010 6346011 a 0 + 6 6 chr1 7250271 7256519 a 0 - 7 7 chr15 4568365 4577519 a 0 - 8 8 chr17 7054047 7060625 a 0 - 9 9 chr19 7019821 7024212 a 0 - 10 10 chr3 8235258 8239581 a 0 - 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4117770 | 4117771 | a | 0 | + | | chr1 | 6346010 | 6346011 | a | 0 | + | | chr1 | 1 | 5511 | a | 0 | + | | chr1 | 7250271 | 7256519 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr3 | 8235258 | 8239581 | a | 0 | - | | chr15 | 4568365 | 4577519 | a | 0 | - | | chr17 | 7054047 | 7060625 | a | 0 | - | | chr19 | 7019821 | 7024212 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3712167 | 3717928 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp2iyh1ik8/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 3712167 3717928 a 0 - 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3712167 | 3717928 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9139575 | 9144808 | a | 0 | + | | chr1 | 774334 | 781539 | a | 0 | + | | chr3 | 1961574 | 1966807 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpcqneq9l3/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 774334 781539 a 0 + 1 1 chr1 9139575 9144808 a 0 + 2 2 chr3 1961574 1966807 a 0 - 3 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9139575 | 9144808 | a | 0 | + | | chr1 | 774334 | 781539 | a | 0 | + | | chr3 | 1961574 | 1966807 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6808744 | 6811040 | a | 0 | + | | chr1 | 2479611 | 2484619 | a | 0 | + | | chr1 | 2479611 | 2486138 | a | 0 | + | | chr1 | 8301759 | 8303418 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr11 | 8406835 | 8410172 | a | 0 | + | | chr16 | 2479611 | 2480481 | a | 0 | - | | chr17 | 2479611 | 2487023 | a | 0 | - | | chr19 | 2479611 | 2479612 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpwf17g6cs/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2479611 2480478 a 0 - 1 1 chr1 2479611 2481907 a 0 - 1 2 chr1 2479611 2484619 a 0 + 1 3 chr1 2479611 2486138 a 0 + 1 4 chr1 6808744 6811040 a 0 + 2 5 chr1 7502591 7511609 a 0 - 3 6 chr1 8301759 8303418 a 0 - 4 7 chr11 8406835 8410172 a 0 + 5 8 chr16 2479611 2480481 a 0 - 6 9 chr17 2479611 2487023 a 0 - 7 10 chr19 2479611 2479612 a 0 - 8 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6808744 | 6811040 | a | 0 | + | | chr1 | 2479611 | 2484619 | a | 0 | + | | chr1 | 2479611 | 2486138 | a | 0 | + | | chr1 | 8301759 | 8303418 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr11 | 8406835 | 8410172 | a | 0 | + | | chr16 | 2479611 | 2480481 | a | 0 | - | | chr17 | 2479611 | 2487023 | a | 0 | - | | chr19 | 2479611 | 2479612 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9488297 | 9494663 | a | 0 | + | | chr10 | 9488297 | 9497088 | a | 0 | - | | chr16 | 9488297 | 9494287 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpoqd56cml/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 9488297 9494663 a 0 + 1 1 chr10 9488297 9497088 a 0 - 2 2 chr16 9488297 9494287 a 0 + 3 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9488297 | 9494663 | a | 0 | + | | chr10 | 9488297 | 9497088 | a | 0 | - | | chr16 | 9488297 | 9494287 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2135407 | 2137614 | a | 0 | + | | chr1 | 2135407 | 2137614 | a | 0 | + | | chr1 | 2135407 | 2136962 | a | 0 | + | | chr1 | 2135407 | 2137614 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr3 | 2135407 | 2137614 | a | 0 | - | | chr11 | 2135407 | 2141403 | a | 0 | + | | chr14 | 2135407 | 2143157 | a | 0 | + | | chrY | 2135407 | 2139117 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpbympx7on/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2135407 2136962 a 0 + 1 1 chr1 2135407 2137614 a 0 + 1 2 chr1 2135407 2137614 a 0 + 1 3 chr1 2135407 2137614 a 0 + 1 4 chr1 2135407 2137614 a 0 - 1 5 chr1 2135407 2144499 a 0 - 1 6 chr11 2135407 2141403 a 0 + 2 7 chr14 2135407 2143157 a 0 + 3 8 chr2 2135407 2137614 a 0 + 4 9 chr3 2135407 2137614 a 0 - 5 10 chrY 2135407 2139117 a 0 + 6 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2135407 | 2137614 | a | 0 | + | | chr1 | 2135407 | 2137614 | a | 0 | + | | chr1 | 2135407 | 2136962 | a | 0 | + | | chr1 | 2135407 | 2137614 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr3 | 2135407 | 2137614 | a | 0 | - | | chr11 | 2135407 | 2141403 | a | 0 | + | | chr14 | 2135407 | 2143157 | a | 0 | + | | chrY | 2135407 | 2139117 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5832370 | 5842369 | a | 0 | + | | chr1 | 1207559 | 1208273 | a | 0 | - | | chr14 | 1644734 | 1653858 | a | 0 | + | | chr14 | 5693819 | 5695711 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpthpy5pbn/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1207559 1208273 a 0 - 1 1 chr1 5832370 5842369 a 0 + 2 2 chr14 1644734 1653858 a 0 + 3 3 chr14 5693819 5695711 a 0 + 4 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5832370 | 5842369 | a | 0 | + | | chr1 | 1207559 | 1208273 | a | 0 | - | | chr14 | 1644734 | 1653858 | a | 0 | + | | chr14 | 5693819 | 5695711 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5645714 | 5648812 | a | 0 | + | | chr1 | 5162719 | 5164569 | a | 0 | - | | chr1 | 5424161 | 5427901 | a | 0 | - | | chr1 | 497933 | 505438 | a | 0 | - | | chr1 | 2134793 | 2136030 | a | 0 | - | | chr4 | 3890446 | 3890915 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp_1ksl8ck/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 497933 505438 a 0 - 1 1 chr1 2134793 2136030 a 0 - 2 2 chr1 5162719 5164569 a 0 - 3 3 chr1 5424161 5427901 a 0 - 4 4 chr1 5645714 5648812 a 0 + 5 5 chr4 3890446 3890915 a 0 - 6 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5645714 | 5648812 | a | 0 | + | | chr1 | 5162719 | 5164569 | a | 0 | - | | chr1 | 5424161 | 5427901 | a | 0 | - | | chr1 | 497933 | 505438 | a | 0 | - | | chr1 | 2134793 | 2136030 | a | 0 | - | | chr4 | 3890446 | 3890915 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9839707 | 9844565 | a | 0 | + | | chr1 | 2059135 | 2059730 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpdhllrl7w/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2059135 2059730 a 0 - 1 1 chr1 9839707 9844565 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9839707 | 9844565 | a | 0 | + | | chr1 | 2059135 | 2059730 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5802098 | 5802330 | a | 0 | + | | chr1 | 679531 | 683697 | a | 0 | + | | chr1 | 1510539 | 1514171 | a | 0 | + | | chr1 | 6318066 | 6326937 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr1 | 9349336 | 9349406 | a | 0 | - | | chr1 | 1 | 9113 | a | 0 | - | | chr1 | 1486752 | 1490470 | a | 0 | - | | chr1 | 6635686 | 6638459 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpr5den9uv/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 9113 a 0 - 1 1 chr1 679531 683697 a 0 + 2 2 chr1 1486752 1490470 a 0 - 3 3 chr1 1510539 1514171 a 0 + 4 4 chr1 5802098 5802330 a 0 + 5 5 chr1 6318066 6326937 a 0 - 6 6 chr1 6635686 6638459 a 0 - 7 7 chr1 9349336 9349406 a 0 - 8 8 chr13 4615441 4615604 a 0 + 9 9 chr9 713715 721288 a 0 + 10 10 chr9 1813327 1821739 a 0 + 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5802098 | 5802330 | a | 0 | + | | chr1 | 679531 | 683697 | a | 0 | + | | chr1 | 1510539 | 1514171 | a | 0 | + | | chr1 | 6318066 | 6326937 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr1 | 9349336 | 9349406 | a | 0 | - | | chr1 | 1 | 9113 | a | 0 | - | | chr1 | 1486752 | 1490470 | a | 0 | - | | chr1 | 6635686 | 6638459 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7482765 | 7492765 | a | 0 | - | | chr14 | 2986931 | 2992102 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp7n55kjqd/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 7482765 7492765 a 0 - 1 1 chr14 2986931 2992102 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7482765 | 7492765 | a | 0 | - | | chr14 | 2986931 | 2992102 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8742893 | 8750344 | a | 0 | + | | chr1 | 3886250 | 3895850 | a | 0 | - | | chr1 | 5909811 | 5916635 | a | 0 | - | | chr1 | 8458661 | 8464800 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr5 | 3178392 | 3181937 | a | 0 | + | | chr5 | 9999999 | 10004494 | a | 0 | - | | chr6 | 6822268 | 6831329 | a | 0 | + | | chr9 | 4802240 | 4807001 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 10 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpp6bdao5o/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 3886250 3895850 a 0 - 1 1 chr1 5909811 5916635 a 0 - 2 2 chr1 6822268 6829314 a 0 - 3 3 chr1 8458661 8464800 a 0 - 4 4 chr1 8742893 8750344 a 0 + 5 5 chr5 3178392 3181937 a 0 + 6 6 chr5 9999999 10004494 a 0 - 7 7 chr6 6822268 6831329 a 0 + 8 8 chr9 4802240 4807001 a 0 + 9 9 chrX 2393053 2401381 a 0 - 10 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8742893 | 8750344 | a | 0 | + | | chr1 | 3886250 | 3895850 | a | 0 | - | | chr1 | 5909811 | 5916635 | a | 0 | - | | chr1 | 8458661 | 8464800 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr5 | 3178392 | 3181937 | a | 0 | + | | chr5 | 9999999 | 10004494 | a | 0 | - | | chr6 | 6822268 | 6831329 | a | 0 | + | | chr9 | 4802240 | 4807001 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 10 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6096187 | 6098525 | a | 0 | + | | chr3 | 6118256 | 6120677 | a | 0 | - | | chrM | 3670494 | 3676488 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp0ha8isjc/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 6096187 6098525 a 0 + 1 1 chr3 6118256 6120677 a 0 - 2 2 chrM 3670494 3676488 a 0 + 3 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6096187 | 6098525 | a | 0 | + | | chr3 | 6118256 | 6120677 | a | 0 | - | | chrM | 3670494 | 3676488 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8206723 | 8213919 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp279jrxre/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 8206723 8213919 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8206723 | 8213919 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4998945 | 5002804 | a | 0 | + | | chr1 | 6160839 | 6166614 | a | 0 | + | | chr1 | 6967109 | 6970067 | a | 0 | + | | chr1 | 8694883 | 8700454 | a | 0 | + | | chr1 | 8030682 | 8030851 | a | 0 | - | | chr1 | 1881750 | 1885054 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp_ow20buw/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1881750 1885054 a 0 - 1 1 chr1 4998945 5002804 a 0 + 2 2 chr1 6160839 6166614 a 0 + 3 3 chr1 6967109 6970067 a 0 + 4 4 chr1 8030682 8030851 a 0 - 5 5 chr1 8694883 8700454 a 0 + 6 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4998945 | 5002804 | a | 0 | + | | chr1 | 6160839 | 6166614 | a | 0 | + | | chr1 | 6967109 | 6970067 | a | 0 | + | | chr1 | 8694883 | 8700454 | a | 0 | + | | chr1 | 8030682 | 8030851 | a | 0 | - | | chr1 | 1881750 | 1885054 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3624530 | 3630856 | a | 0 | + | | chr1 | 730183 | 735599 | a | 0 | + | | chr1 | 3363350 | 3365639 | a | 0 | - | | chr1 | 1415506 | 1418185 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr1 | 3363350 | 3365639 | a | 0 | - | | chr1 | 1415506 | 1418185 | a | 0 | - | | chr1 | 1037633 | 1039172 | a | 0 | - | | chr1 | 857710 | 859009 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 9 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpwzmej4ck/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 730183 735599 a 0 + 1 1 chr1 857710 859009 a 0 - 2 2 chr1 1037633 1039172 a 0 - 3 3 chr1 1415506 1418185 a 0 - 4 4 chr1 3363350 3365639 a 0 - 5 5 chr1 3624530 3630856 a 0 + 6 6 chr22 9758095 9760692 a 0 + 7 7 chr8 6214686 6215985 a 0 - 8 8 chrM 10000000 10001299 a 0 - 9 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3624530 | 3630856 | a | 0 | + | | chr1 | 730183 | 735599 | a | 0 | + | | chr1 | 3363350 | 3365639 | a | 0 | - | | chr1 | 1415506 | 1418185 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr1 | 3363350 | 3365639 | a | 0 | - | | chr1 | 1415506 | 1418185 | a | 0 | - | | chr1 | 1037633 | 1039172 | a | 0 | - | | chr1 | 857710 | 859009 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 9 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8674208 | 8676552 | a | 0 | + | | chr1 | 6824998 | 6827342 | a | 0 | + | | chr7 | 5442870 | 5445214 | a | 0 | + | | chr14 | 8168041 | 8170385 | a | 0 | + | | chr18 | 778332 | 780676 | a | 0 | + | | chr19 | 5085217 | 5087561 | a | 0 | - | | chr21 | 9822922 | 9825266 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 7 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpd1jntz43/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 6824998 6827342 a 0 + 1 1 chr1 8674208 8676552 a 0 + 2 2 chr14 8168041 8170385 a 0 + 3 3 chr18 778332 780676 a 0 + 4 4 chr19 5085217 5087561 a 0 - 5 5 chr21 9822922 9825266 a 0 - 6 6 chr7 5442870 5445214 a 0 + 7 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8674208 | 8676552 | a | 0 | + | | chr1 | 6824998 | 6827342 | a | 0 | + | | chr7 | 5442870 | 5445214 | a | 0 | + | | chr14 | 8168041 | 8170385 | a | 0 | + | | chr18 | 778332 | 780676 | a | 0 | + | | chr19 | 5085217 | 5087561 | a | 0 | - | | chr21 | 9822922 | 9825266 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 7 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 7205 | a | 0 | + | | chr1 | 8897159 | 8901007 | a | 0 | + | | chr6 | 9498512 | 9508512 | a | 0 | + | | chr18 | 8124014 | 8131027 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp0kjbwvw4/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 7205 a 0 + 1 1 chr1 8897159 8901007 a 0 + 2 2 chr18 8124014 8131027 a 0 + 3 3 chr6 9498512 9508512 a 0 + 4 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 7205 | a | 0 | + | | chr1 | 8897159 | 8901007 | a | 0 | + | | chr6 | 9498512 | 9508512 | a | 0 | + | | chr18 | 8124014 | 8131027 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3094151 | 3097945 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpdft420v8/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 3094151 3097945 a 0 - 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3094151 | 3097945 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9922642 | 9923596 | a | 0 | + | | chr1 | 9056443 | 9060309 | a | 0 | + | | chr1 | 155074 | 161738 | a | 0 | - | | chr11 | 10000000 | 10005834 | a | 0 | + | | chr14 | 7566008 | 7572769 | a | 0 | + | | chr14 | 7821055 | 7821189 | a | 0 | + | | chr21 | 4194732 | 4196185 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 7 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp89dqdh3p/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 155074 161738 a 0 - 1 1 chr1 9056443 9060309 a 0 + 2 2 chr1 9922642 9923596 a 0 + 3 3 chr11 10000000 10005834 a 0 + 4 4 chr14 7566008 7572769 a 0 + 5 5 chr14 7821055 7821189 a 0 + 6 6 chr21 4194732 4196185 a 0 + 7 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9922642 | 9923596 | a | 0 | + | | chr1 | 9056443 | 9060309 | a | 0 | + | | chr1 | 155074 | 161738 | a | 0 | - | | chr11 | 10000000 | 10005834 | a | 0 | + | | chr14 | 7566008 | 7572769 | a | 0 | + | | chr14 | 7821055 | 7821189 | a | 0 | + | | chr21 | 4194732 | 4196185 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 7 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5631143 | 5637841 | a | 0 | + | | chr1 | 3789641 | 3799428 | a | 0 | - | | chr1 | 2057989 | 2057990 | a | 0 | - | | chr1 | 3416400 | 3422293 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr19 | 2513345 | 2522904 | a | 0 | - | | chr22 | 7119597 | 7127359 | a | 0 | + | | chrX | 9999999 | 10006772 | a | 0 | + | | chrX | 9999999 | 10001415 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 9 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpnkgge5c_/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2057989 2057990 a 0 - 1 1 chr1 3416400 3422293 a 0 - 2 2 chr1 3789641 3799428 a 0 - 3 3 chr1 5631143 5637841 a 0 + 4 4 chr14 5093133 5094961 a 0 - 5 5 chr19 2513345 2522904 a 0 - 6 6 chr22 7119597 7127359 a 0 + 7 7 chrX 9999999 10001415 a 0 - 8 8 chrX 9999999 10006772 a 0 + 8 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5631143 | 5637841 | a | 0 | + | | chr1 | 3789641 | 3799428 | a | 0 | - | | chr1 | 2057989 | 2057990 | a | 0 | - | | chr1 | 3416400 | 3422293 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr19 | 2513345 | 2522904 | a | 0 | - | | chr22 | 7119597 | 7127359 | a | 0 | + | | chrX | 9999999 | 10006772 | a | 0 | + | | chrX | 9999999 | 10001415 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 9 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1794519 | 1798203 | a | 0 | - | | chr14 | 4626009 | 4629436 | a | 0 | + | | chr19 | 4559810 | 4566458 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpbrgkrucu/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1794519 1798203 a 0 - 1 1 chr14 4626009 4629436 a 0 + 2 2 chr19 4559810 4566458 a 0 - 3 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1794519 | 1798203 | a | 0 | - | | chr14 | 4626009 | 4629436 | a | 0 | + | | chr19 | 4559810 | 4566458 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr7 | 7060534 | 7067317 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp3tqzqqmv/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr7 7060534 7067317 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr7 | 7060534 | 7067317 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7173092 | 7179276 | a | 0 | + | | chr1 | 8737974 | 8746766 | a | 0 | + | | chr1 | 4306498 | 4311196 | a | 0 | + | | chr1 | 3832076 | 3837812 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr6 | 6154755 | 6155506 | a | 0 | + | | chr6 | 2388228 | 2396296 | a | 0 | - | | chr12 | 6165711 | 6171427 | a | 0 | + | | chr15 | 10000000 | 10000002 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp__zl06ft/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1504069 1510180 a 0 - 1 1 chr1 3832076 3837812 a 0 + 2 2 chr1 4306498 4311196 a 0 + 3 3 chr1 5506571 5513622 a 0 - 4 4 chr1 7173092 7179276 a 0 + 5 5 chr1 8737974 8746766 a 0 + 6 6 chr12 6165711 6171427 a 0 + 7 7 chr15 10000000 10000002 a 0 - 8 8 chr21 6697269 6697323 a 0 - 9 9 chr6 2388228 2396296 a 0 - 10 10 chr6 6154755 6155506 a 0 + 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7173092 | 7179276 | a | 0 | + | | chr1 | 8737974 | 8746766 | a | 0 | + | | chr1 | 4306498 | 4311196 | a | 0 | + | | chr1 | 3832076 | 3837812 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr6 | 6154755 | 6155506 | a | 0 | + | | chr6 | 2388228 | 2396296 | a | 0 | - | | chr12 | 6165711 | 6171427 | a | 0 | + | | chr15 | 10000000 | 10000002 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7952163 | 7954227 | a | 0 | + | | chr1 | 1 | 6560 | a | 0 | + | | chr1 | 5628916 | 5635049 | a | 0 | + | | chr1 | 7192050 | 7198618 | a | 0 | - | | chr10 | 8766388 | 8772361 | a | 0 | + | | chr18 | 3220475 | 3226043 | a | 0 | + | | chrX | 4190915 | 4196703 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 7 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp5fvf25ad/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 6560 a 0 + 1 1 chr1 5628916 5635049 a 0 + 2 2 chr1 7192050 7198618 a 0 - 3 3 chr1 7952163 7954227 a 0 + 4 4 chr10 8766388 8772361 a 0 + 5 5 chr18 3220475 3226043 a 0 + 6 6 chrX 4190915 4196703 a 0 + 7 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7952163 | 7954227 | a | 0 | + | | chr1 | 1 | 6560 | a | 0 | + | | chr1 | 5628916 | 5635049 | a | 0 | + | | chr1 | 7192050 | 7198618 | a | 0 | - | | chr10 | 8766388 | 8772361 | a | 0 | + | | chr18 | 3220475 | 3226043 | a | 0 | + | | chrX | 4190915 | 4196703 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 7 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4952315 | 4958989 | a | 0 | + | | chr20 | 9056955 | 9060459 | a | 0 | - | | chr20 | 1246271 | 1246962 | a | 0 | - | | chr22 | 9711070 | 9712189 | a | 0 | - | | chrM | 9711070 | 9714574 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpt0a80no2/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 4952315 4958989 a 0 + 1 1 chr20 1246271 1246962 a 0 - 2 2 chr20 9056955 9060459 a 0 - 3 3 chr22 9711070 9712189 a 0 - 4 4 chrM 9711070 9714574 a 0 - 5 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4952315 | 4958989 | a | 0 | + | | chr20 | 9056955 | 9060459 | a | 0 | - | | chr20 | 1246271 | 1246962 | a | 0 | - | | chr22 | 9711070 | 9712189 | a | 0 | - | | chrM | 9711070 | 9714574 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 995560 | 1002689 | a | 0 | - | | chr15 | 3792333 | 3794783 | a | 0 | - | | chrX | 574386 | 582480 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpp4pfszu6/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 995560 1002689 a 0 - 1 1 chr15 3792333 3794783 a 0 - 2 2 chrX 574386 582480 a 0 + 3 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 995560 | 1002689 | a | 0 | - | | chr15 | 3792333 | 3794783 | a | 0 | - | | chrX | 574386 | 582480 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1019302 | 1020579 | a | 0 | + | | chr1 | 4122569 | 4131767 | a | 0 | - | | chr1 | 1019302 | 1026191 | a | 0 | - | | chr5 | 1019302 | 1022084 | a | 0 | - | | chr7 | 1019302 | 1020329 | a | 0 | - | | chr14 | 1019302 | 1029199 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpvmhhe3j1/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1019302 1020579 a 0 + 1 1 chr1 1019302 1026191 a 0 - 1 2 chr1 4122569 4131767 a 0 - 2 3 chr14 1019302 1029199 a 0 - 3 4 chr5 1019302 1022084 a 0 - 4 5 chr7 1019302 1020329 a 0 - 5 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1019302 | 1020579 | a | 0 | + | | chr1 | 4122569 | 4131767 | a | 0 | - | | chr1 | 1019302 | 1026191 | a | 0 | - | | chr5 | 1019302 | 1022084 | a | 0 | - | | chr7 | 1019302 | 1020329 | a | 0 | - | | chr14 | 1019302 | 1029199 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8492758 | 8501000 | a | 0 | + | | chr1 | 2478381 | 2486366 | a | 0 | - | | chr1 | 834294 | 837131 | a | 0 | - | | chr1 | 4490897 | 4497293 | a | 0 | - | | chr1 | 2570774 | 2571118 | a | 0 | - | | chr8 | 6265462 | 6268299 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpwo9k2_cu/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 834294 837131 a 0 - 1 1 chr1 2478381 2486366 a 0 - 2 2 chr1 2570774 2571118 a 0 - 3 3 chr1 4490897 4497293 a 0 - 4 4 chr1 8492758 8501000 a 0 + 5 5 chr8 6265462 6268299 a 0 - 6 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8492758 | 8501000 | a | 0 | + | | chr1 | 2478381 | 2486366 | a | 0 | - | | chr1 | 834294 | 837131 | a | 0 | - | | chr1 | 4490897 | 4497293 | a | 0 | - | | chr1 | 2570774 | 2571118 | a | 0 | - | | chr8 | 6265462 | 6268299 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr9 | 4885789 | 4891947 | a | 0 | - | | chr12 | 3360135 | 3361588 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpiqybrm_z/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr12 3360135 3361588 a 0 - 1 1 chr9 4885789 4891947 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr9 | 4885789 | 4891947 | a | 0 | - | | chr12 | 3360135 | 3361588 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr21 | 3848817 | 3848818 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpdd7z_ot7/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr21 3848817 3848818 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr21 | 3848817 | 3848818 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6409977 | 6410016 | a | 0 | + | | chr3 | 6409977 | 6412337 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpqcya1cn2/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 6409977 6410016 a 0 + 1 1 chr3 6409977 6412337 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6409977 | 6410016 | a | 0 | + | | chr3 | 6409977 | 6412337 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1124713 | 1124801 | a | 0 | + | | chr1 | 4500689 | 4509592 | a | 0 | + | | chr1 | 2962341 | 2967006 | a | 0 | + | | chr1 | 3552765 | 3562330 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr15 | 9826349 | 9832402 | a | 0 | - | | chrX | 2238419 | 2245338 | a | 0 | + | | chrX | 3892032 | 3893436 | a | 0 | - | | chrX | 8247214 | 8254047 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp3ks16vg3/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1124713 1124801 a 0 + 1 1 chr1 2962341 2967006 a 0 + 2 2 chr1 3552765 3562330 a 0 - 3 3 chr1 4500689 4509592 a 0 + 4 4 chr12 5168162 5171135 a 0 - 5 5 chr15 9826349 9832402 a 0 - 6 6 chr2 3948481 3949055 a 0 + 7 7 chr2 8803729 8808117 a 0 + 8 8 chrX 2238419 2245338 a 0 + 9 9 chrX 3892032 3893436 a 0 - 10 10 chrX 8247214 8254047 a 0 - 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1124713 | 1124801 | a | 0 | + | | chr1 | 4500689 | 4509592 | a | 0 | + | | chr1 | 2962341 | 2967006 | a | 0 | + | | chr1 | 3552765 | 3562330 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr15 | 9826349 | 9832402 | a | 0 | - | | chrX | 2238419 | 2245338 | a | 0 | + | | chrX | 3892032 | 3893436 | a | 0 | - | | chrX | 8247214 | 8254047 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 856047 | 858550 | a | 0 | - | | chr1 | 2706374 | 2709773 | a | 0 | - | | chrX | 6469928 | 6472667 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpx1agdv63/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 856047 858550 a 0 - 1 1 chr1 2706374 2709773 a 0 - 2 2 chrX 6469928 6472667 a 0 - 3 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 856047 | 858550 | a | 0 | - | | chr1 | 2706374 | 2709773 | a | 0 | - | | chrX | 6469928 | 6472667 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5517176 | 5523302 | a | 0 | + | | chr1 | 8946518 | 8953621 | a | 0 | + | | chr1 | 2840855 | 2849409 | a | 0 | - | | chr1 | 2342239 | 2348618 | a | 0 | - | | chr5 | 2840855 | 2850016 | a | 0 | + | | chr16 | 38937 | 39088 | a | 0 | + | | chr17 | 2840855 | 2840856 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 7 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp9o6u8ihl/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2342239 2348618 a 0 - 1 1 chr1 2840855 2849409 a 0 - 2 2 chr1 5517176 5523302 a 0 + 3 3 chr1 8946518 8953621 a 0 + 4 4 chr16 38937 39088 a 0 + 5 5 chr17 2840855 2840856 a 0 + 6 6 chr5 2840855 2850016 a 0 + 7 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5517176 | 5523302 | a | 0 | + | | chr1 | 8946518 | 8953621 | a | 0 | + | | chr1 | 2840855 | 2849409 | a | 0 | - | | chr1 | 2342239 | 2348618 | a | 0 | - | | chr5 | 2840855 | 2850016 | a | 0 | + | | chr16 | 38937 | 39088 | a | 0 | + | | chr17 | 2840855 | 2840856 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 7 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3478307 | 3478915 | a | 0 | + | | chr1 | 3478307 | 3487168 | a | 0 | - | | chr1 | 7323837 | 7331980 | a | 0 | - | | chr1 | 3478307 | 3479863 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr2 | 3478307 | 3480765 | a | 0 | + | | chr6 | 3478307 | 3479850 | a | 0 | - | | chr15 | 3478307 | 3484347 | a | 0 | + | | chr22 | 7771438 | 7777089 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 9 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp1sa7xfd6/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 3478307 3478915 a 0 + 1 1 chr1 3478307 3479863 a 0 - 1 2 chr1 3478307 3487073 a 0 - 1 3 chr1 3478307 3487168 a 0 - 1 4 chr1 7323837 7331980 a 0 - 2 5 chr15 3478307 3484347 a 0 + 3 6 chr2 3478307 3480765 a 0 + 4 7 chr22 7771438 7777089 a 0 + 5 8 chr6 3478307 3479850 a 0 - 6 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3478307 | 3478915 | a | 0 | + | | chr1 | 3478307 | 3487168 | a | 0 | - | | chr1 | 7323837 | 7331980 | a | 0 | - | | chr1 | 3478307 | 3479863 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr2 | 3478307 | 3480765 | a | 0 | + | | chr6 | 3478307 | 3479850 | a | 0 | - | | chr15 | 3478307 | 3484347 | a | 0 | + | | chr22 | 7771438 | 7777089 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 9 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7140982 | 7143125 | a | 0 | + | | chr1 | 7410425 | 7419870 | a | 0 | + | | chr1 | 1152860 | 1160607 | a | 0 | + | | chr1 | 1595357 | 1601159 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr8 | 9999999 | 10003039 | a | 0 | + | | chr8 | 2 | 3754 | a | 0 | + | | chr8 | 4172375 | 4175773 | a | 0 | - | | chr9 | 2178883 | 2187815 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 10 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp0f7dxd0e/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1152860 1160607 a 0 + 1 1 chr1 1595357 1601159 a 0 + 2 2 chr1 6505736 6514497 a 0 - 3 3 chr1 7140982 7143125 a 0 + 4 4 chr1 7410425 7419870 a 0 + 5 5 chr1 8034702 8038182 a 0 - 6 6 chr8 2 3754 a 0 + 7 7 chr8 4172375 4175773 a 0 - 8 8 chr8 9999999 10003039 a 0 + 9 9 chr9 2178883 2187815 a 0 + 10 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7140982 | 7143125 | a | 0 | + | | chr1 | 7410425 | 7419870 | a | 0 | + | | chr1 | 1152860 | 1160607 | a | 0 | + | | chr1 | 1595357 | 1601159 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr8 | 9999999 | 10003039 | a | 0 | + | | chr8 | 2 | 3754 | a | 0 | + | | chr8 | 4172375 | 4175773 | a | 0 | - | | chr9 | 2178883 | 2187815 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 10 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2338554 | 2342950 | a | 0 | + | | chr1 | 8123686 | 8131406 | a | 0 | + | | chr16 | 9320946 | 9330936 | a | 0 | + | | chr20 | 1355688 | 1357248 | a | 0 | + | | chr20 | 9562439 | 9568735 | a | 0 | - | | chr21 | 2338554 | 2348215 | a | 0 | + | | chrX | 6172391 | 6181144 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 7 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpfcrvjwlp/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2338554 2342950 a 0 + 1 1 chr1 8123686 8131406 a 0 + 2 2 chr16 9320946 9330936 a 0 + 3 3 chr20 1355688 1357248 a 0 + 4 4 chr20 9562439 9568735 a 0 - 5 5 chr21 2338554 2348215 a 0 + 6 6 chrX 6172391 6181144 a 0 + 7 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2338554 | 2342950 | a | 0 | + | | chr1 | 8123686 | 8131406 | a | 0 | + | | chr16 | 9320946 | 9330936 | a | 0 | + | | chr20 | 1355688 | 1357248 | a | 0 | + | | chr20 | 9562439 | 9568735 | a | 0 | - | | chr21 | 2338554 | 2348215 | a | 0 | + | | chrX | 6172391 | 6181144 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 7 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4239438 | 4249437 | a | 0 | + | | chr1 | 9671590 | 9676576 | a | 0 | - | | chr1 | 4368228 | 4375247 | a | 0 | - | | chr1 | 1 | 9184 | a | 0 | - | | chr1 | 9292119 | 9296912 | a | 0 | - | | chr1 | 4860369 | 4861251 | a | 0 | - | | chr1 | 6418320 | 6423510 | a | 0 | - | | chr1 | 5030167 | 5034899 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 8 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpkb8092fc/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 9184 a 0 - 1 1 chr1 4239438 4249437 a 0 + 2 2 chr1 4368228 4375247 a 0 - 3 3 chr1 4860369 4861251 a 0 - 4 4 chr1 5030167 5034899 a 0 - 5 5 chr1 6418320 6423510 a 0 - 6 6 chr1 9292119 9296912 a 0 - 7 7 chr1 9671590 9676576 a 0 - 8 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4239438 | 4249437 | a | 0 | + | | chr1 | 9671590 | 9676576 | a | 0 | - | | chr1 | 4368228 | 4375247 | a | 0 | - | | chr1 | 1 | 9184 | a | 0 | - | | chr1 | 9292119 | 9296912 | a | 0 | - | | chr1 | 4860369 | 4861251 | a | 0 | - | | chr1 | 6418320 | 6423510 | a | 0 | - | | chr1 | 5030167 | 5034899 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 8 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1244414 | 1253173 | a | 0 | + | | chr1 | 4723308 | 4728880 | a | 0 | + | | chr1 | 345591 | 345833 | a | 0 | - | | chr1 | 5888836 | 5898589 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr5 | 39286 | 47834 | a | 0 | - | | chr5 | 9699529 | 9699938 | a | 0 | - | | chr5 | 9639325 | 9645425 | a | 0 | - | | chr5 | 7521888 | 7526071 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp8rd_f17x/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 345591 345833 a 0 - 1 1 chr1 1244414 1253173 a 0 + 2 2 chr1 4723308 4728880 a 0 + 3 3 chr1 5888836 5898589 a 0 - 4 4 chr10 4328693 4336415 a 0 - 5 5 chr19 1794936 1803419 a 0 + 6 6 chr3 3593167 3602019 a 0 - 7 7 chr5 39286 47834 a 0 - 8 8 chr5 7521888 7526071 a 0 - 9 9 chr5 9639325 9645425 a 0 - 10 10 chr5 9699529 9699938 a 0 - 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1244414 | 1253173 | a | 0 | + | | chr1 | 4723308 | 4728880 | a | 0 | + | | chr1 | 345591 | 345833 | a | 0 | - | | chr1 | 5888836 | 5898589 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr5 | 39286 | 47834 | a | 0 | - | | chr5 | 9699529 | 9699938 | a | 0 | - | | chr5 | 9639325 | 9645425 | a | 0 | - | | chr5 | 7521888 | 7526071 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1303363 | 1308636 | a | 0 | + | | chr1 | 8956111 | 8961384 | a | 0 | + | | chr1 | 1 | 5274 | a | 0 | + | | chr1 | 3101727 | 3107000 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr1 | 3101727 | 3107000 | a | 0 | + | | chr1 | 2699817 | 2705090 | a | 0 | - | | chr1 | 9008451 | 9013724 | a | 0 | - | | chr1 | 8503968 | 8509964 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 9 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmplb7tb_3i/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 5274 a 0 + 1 1 chr1 1303363 1308636 a 0 + 2 2 chr1 2699817 2705090 a 0 - 3 3 chr1 3101727 3107000 a 0 + 4 4 chr1 8503968 8509964 a 0 - 5 5 chr1 8956111 8961384 a 0 + 6 6 chr1 9008451 9013724 a 0 - 7 7 chr11 4742440 4747713 a 0 - 8 8 chr7 9851723 9856996 a 0 - 9 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1303363 | 1308636 | a | 0 | + | | chr1 | 8956111 | 8961384 | a | 0 | + | | chr1 | 1 | 5274 | a | 0 | + | | chr1 | 3101727 | 3107000 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr1 | 3101727 | 3107000 | a | 0 | + | | chr1 | 2699817 | 2705090 | a | 0 | - | | chr1 | 9008451 | 9013724 | a | 0 | - | | chr1 | 8503968 | 8509964 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 9 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6151770 | 6159928 | a | 0 | - | | chr1 | 1584145 | 1591654 | a | 0 | - | | chr1 | 9808920 | 9816429 | a | 0 | - | | chr1 | 10000000 | 10007509 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr1 | 3463832 | 3464328 | a | 0 | - | | chr1 | 8181805 | 8185502 | a | 0 | - | | chr1 | 2705820 | 2706117 | a | 0 | - | | chr1 | 1319213 | 1326362 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp5p1lr1d9/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1319213 1326362 a 0 - 1 1 chr1 1584145 1591654 a 0 - 2 2 chr1 2705820 2706117 a 0 - 3 3 chr1 3463832 3464328 a 0 - 4 4 chr1 3783142 3790651 a 0 - 5 5 chr1 6151770 6159928 a 0 - 6 6 chr1 6456155 6463664 a 0 - 7 7 chr1 7902261 7902702 a 0 - 8 8 chr1 8181805 8185502 a 0 - 9 9 chr1 9808920 9816429 a 0 - 10 10 chr1 10000000 10007509 a 0 - 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6151770 | 6159928 | a | 0 | - | | chr1 | 1584145 | 1591654 | a | 0 | - | | chr1 | 9808920 | 9816429 | a | 0 | - | | chr1 | 10000000 | 10007509 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr1 | 3463832 | 3464328 | a | 0 | - | | chr1 | 8181805 | 8185502 | a | 0 | - | | chr1 | 2705820 | 2706117 | a | 0 | - | | chr1 | 1319213 | 1326362 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 626302 | 626830 | a | 0 | + | | chr15 | 4769124 | 4769171 | a | 0 | + | | chr20 | 3602309 | 3607892 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpawosylua/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 626302 626830 a 0 + 1 1 chr15 4769124 4769171 a 0 + 2 2 chr20 3602309 3607892 a 0 - 3 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 626302 | 626830 | a | 0 | + | | chr15 | 4769124 | 4769171 | a | 0 | + | | chr20 | 3602309 | 3607892 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1447066 | 1448908 | a | 0 | - | | chr19 | 9145940 | 9148879 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpungusvs8/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1447066 1448908 a 0 - 1 1 chr19 9145940 9148879 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1447066 | 1448908 | a | 0 | - | | chr19 | 9145940 | 9148879 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9910591 | 9916050 | a | 0 | + | | chr1 | 8044596 | 8048551 | a | 0 | + | | chr1 | 9425159 | 9433066 | a | 0 | + | | chr1 | 9425159 | 9432286 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr4 | 1 | 4061 | a | 0 | - | | chr9 | 3972406 | 3973951 | a | 0 | + | | chr16 | 8135251 | 8143779 | a | 0 | + | | chrM | 9425159 | 9427387 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 9 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp_mxxqs5f/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 8044596 8048551 a 0 + 1 1 chr1 9425159 9432286 a 0 - 2 2 chr1 9425159 9433066 a 0 + 2 3 chr1 9910591 9916050 a 0 + 3 4 chr1 9999999 10006549 a 0 - 4 5 chr16 8135251 8143779 a 0 + 5 6 chr4 1 4061 a 0 - 6 7 chr9 3972406 3973951 a 0 + 7 8 chrM 9425159 9427387 a 0 + 8 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9910591 | 9916050 | a | 0 | + | | chr1 | 8044596 | 8048551 | a | 0 | + | | chr1 | 9425159 | 9433066 | a | 0 | + | | chr1 | 9425159 | 9432286 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr4 | 1 | 4061 | a | 0 | - | | chr9 | 3972406 | 3973951 | a | 0 | + | | chr16 | 8135251 | 8143779 | a | 0 | + | | chrM | 9425159 | 9427387 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 9 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 199589 | 204374 | a | 0 | + | | chr1 | 2448750 | 2453535 | a | 0 | + | | chr1 | 9780051 | 9784836 | a | 0 | - | | chr1 | 1858911 | 1863443 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr11 | 3812936 | 3819578 | a | 0 | + | | chr21 | 5059099 | 5061412 | a | 0 | - | | chrM | 9545059 | 9552981 | a | 0 | + | | chrX | 7716529 | 7719325 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 7 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpafd7l_3g/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 199589 204374 a 0 + 1 1 chr1 1858911 1863443 a 0 - 2 2 chr1 2448750 2453535 a 0 + 3 3 chr1 8963332 8968117 a 0 - 4 4 chr1 9780051 9784836 a 0 - 5 5 chr11 3812936 3819578 a 0 + 6 6 chr21 5059099 5061412 a 0 - 7 7 chr6 6795557 6801878 a 0 - 8 8 chr8 8376451 8381236 a 0 - 9 9 chrM 9545059 9552981 a 0 + 10 10 chrX 7716529 7719325 a 0 + 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 199589 | 204374 | a | 0 | + | | chr1 | 2448750 | 2453535 | a | 0 | + | | chr1 | 9780051 | 9784836 | a | 0 | - | | chr1 | 1858911 | 1863443 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr11 | 3812936 | 3819578 | a | 0 | + | | chr21 | 5059099 | 5061412 | a | 0 | - | | chrM | 9545059 | 9552981 | a | 0 | + | | chrX | 7716529 | 7719325 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 7 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4123757 | 4125640 | a | 0 | + | | chr1 | 4123757 | 4127710 | a | 0 | + | | chr1 | 4123757 | 4123959 | a | 0 | + | | chr1 | 9137199 | 9145315 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr1 | 4123757 | 4123959 | a | 0 | + | | chr1 | 9137199 | 9145315 | a | 0 | + | | chr1 | 4123757 | 4132271 | a | 0 | - | | chr1 | 1272934 | 1278950 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 9 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmplepacsuq/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1272934 1278950 a 0 - 1 1 chr1 4123757 4123959 a 0 + 2 2 chr1 4123757 4125640 a 0 + 2 3 chr1 4123757 4127710 a 0 + 2 4 chr1 4123757 4132271 a 0 - 2 5 chr1 9137199 9145315 a 0 + 3 6 chr13 4123757 4131643 a 0 + 4 7 chr18 5305958 5315222 a 0 - 5 8 chr9 4123757 4128169 a 0 + 6 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4123757 | 4125640 | a | 0 | + | | chr1 | 4123757 | 4127710 | a | 0 | + | | chr1 | 4123757 | 4123959 | a | 0 | + | | chr1 | 9137199 | 9145315 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr1 | 4123757 | 4123959 | a | 0 | + | | chr1 | 9137199 | 9145315 | a | 0 | + | | chr1 | 4123757 | 4132271 | a | 0 | - | | chr1 | 1272934 | 1278950 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 9 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 10000000 | 10003778 | a | 0 | - | | chr1 | 9153070 | 9158502 | a | 0 | - | | chr9 | 9153070 | 9161377 | a | 0 | + | | chr15 | 5372869 | 5375135 | a | 0 | - | | chr16 | 9153070 | 9154293 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp1bhz4yf_/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 9153070 9158502 a 0 - 1 1 chr1 10000000 10003778 a 0 - 2 2 chr15 5372869 5375135 a 0 - 3 3 chr16 9153070 9154293 a 0 + 4 4 chr9 9153070 9161377 a 0 + 5 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 10000000 | 10003778 | a | 0 | - | | chr1 | 9153070 | 9158502 | a | 0 | - | | chr9 | 9153070 | 9161377 | a | 0 | + | | chr15 | 5372869 | 5375135 | a | 0 | - | | chr16 | 9153070 | 9154293 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6729686 | 6736367 | a | 0 | - | | chr16 | 4998161 | 5004240 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpfkepong1/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 6729686 6736367 a 0 - 1 1 chr16 4998161 5004240 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6729686 | 6736367 | a | 0 | - | | chr16 | 4998161 | 5004240 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1116293 | 1117928 | a | 0 | + | | chr1 | 1116293 | 1117928 | a | 0 | + | | chr1 | 3248035 | 3249670 | a | 0 | + | | chr1 | 1116293 | 1117928 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr9 | 3839231 | 3840866 | a | 0 | - | | chr19 | 1116293 | 1117928 | a | 0 | - | | chr21 | 1116293 | 1117928 | a | 0 | - | | chrM | 1116293 | 1117928 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmptsf7vcbs/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1116293 1117928 a 0 + 1 1 chr1 1116293 1117928 a 0 + 1 2 chr1 1116293 1117928 a 0 + 1 3 chr1 1116293 1117928 a 0 - 1 4 chr1 3248035 3249670 a 0 + 2 5 chr1 9047203 9048838 a 0 - 3 6 chr19 1116293 1117928 a 0 - 4 7 chr2 9568734 9570369 a 0 + 5 8 chr21 1116293 1117928 a 0 - 6 9 chr9 3839231 3840866 a 0 - 7 10 chrM 1116293 1117928 a 0 + 8 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1116293 | 1117928 | a | 0 | + | | chr1 | 1116293 | 1117928 | a | 0 | + | | chr1 | 3248035 | 3249670 | a | 0 | + | | chr1 | 1116293 | 1117928 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr9 | 3839231 | 3840866 | a | 0 | - | | chr19 | 1116293 | 1117928 | a | 0 | - | | chr21 | 1116293 | 1117928 | a | 0 | - | | chrM | 1116293 | 1117928 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8997460 | 9002535 | a | 0 | - | | chr1 | 2436553 | 2442220 | a | 0 | - | | chr1 | 3877506 | 3880385 | a | 0 | - | | chr1 | 2 | 5077 | a | 0 | - | | chr14 | 9080645 | 9089790 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpqfluaywg/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2 5077 a 0 - 1 1 chr1 2436553 2442220 a 0 - 2 2 chr1 3877506 3880385 a 0 - 3 3 chr1 8997460 9002535 a 0 - 4 4 chr14 9080645 9089790 a 0 + 5 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8997460 | 9002535 | a | 0 | - | | chr1 | 2436553 | 2442220 | a | 0 | - | | chr1 | 3877506 | 3880385 | a | 0 | - | | chr1 | 2 | 5077 | a | 0 | - | | chr14 | 9080645 | 9089790 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3026629 | 3029636 | a | 0 | + | | chr1 | 9265298 | 9275279 | a | 0 | + | | chr1 | 8562691 | 8562698 | a | 0 | + | | chr1 | 2559049 | 2559829 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr1 | 2559049 | 2559829 | a | 0 | - | | chr1 | 7042967 | 7050777 | a | 0 | - | | chr1 | 528516 | 535956 | a | 0 | - | | chr1 | 5175335 | 5183779 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 9 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp7befgxt1/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 528516 535956 a 0 - 1 1 chr1 2559049 2559829 a 0 - 2 2 chr1 3026629 3029636 a 0 + 3 3 chr1 5175335 5183779 a 0 - 4 4 chr1 7042967 7050777 a 0 - 5 5 chr1 8562691 8562698 a 0 + 6 6 chr1 9265298 9275279 a 0 + 7 7 chr16 3822941 3824461 a 0 + 8 8 chrM 8778795 8783365 a 0 + 9 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3026629 | 3029636 | a | 0 | + | | chr1 | 9265298 | 9275279 | a | 0 | + | | chr1 | 8562691 | 8562698 | a | 0 | + | | chr1 | 2559049 | 2559829 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr1 | 2559049 | 2559829 | a | 0 | - | | chr1 | 7042967 | 7050777 | a | 0 | - | | chr1 | 528516 | 535956 | a | 0 | - | | chr1 | 5175335 | 5183779 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 9 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9999999 | 10007410 | a | 0 | + | | chr1 | 6778505 | 6778507 | a | 0 | + | | chr1 | 9262385 | 9269080 | a | 0 | + | | chr1 | 3479676 | 3487236 | a | 0 | + | | chr1 | 5115633 | 5124892 | a | 0 | - | | chr7 | 6551301 | 6561100 | a | 0 | + | | chr12 | 8437333 | 8444468 | a | 0 | - | | chrX | 1789104 | 1790625 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 8 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpc0ux0guq/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 3479676 3487236 a 0 + 1 1 chr1 5115633 5124892 a 0 - 2 2 chr1 6778505 6778507 a 0 + 3 3 chr1 9262385 9269080 a 0 + 4 4 chr1 9999999 10007410 a 0 + 5 5 chr12 8437333 8444468 a 0 - 6 6 chr7 6551301 6561100 a 0 + 7 7 chrX 1789104 1790625 a 0 + 8 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9999999 | 10007410 | a | 0 | + | | chr1 | 6778505 | 6778507 | a | 0 | + | | chr1 | 9262385 | 9269080 | a | 0 | + | | chr1 | 3479676 | 3487236 | a | 0 | + | | chr1 | 5115633 | 5124892 | a | 0 | - | | chr7 | 6551301 | 6561100 | a | 0 | + | | chr12 | 8437333 | 8444468 | a | 0 | - | | chrX | 1789104 | 1790625 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 8 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7915954 | 7917956 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpudohqbe_/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 7915954 7917956 a 0 - 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7915954 | 7917956 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7448040 | 7453318 | a | 0 | - | | chr1 | 7396910 | 7398152 | a | 0 | - | | chr1 | 7749391 | 7752779 | a | 0 | - | | chr4 | 6423904 | 6432723 | a | 0 | - | | chrY | 2909080 | 2911300 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp6e51n3xq/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 7396910 7398152 a 0 - 1 1 chr1 7448040 7453318 a 0 - 2 2 chr1 7749391 7752779 a 0 - 3 3 chr4 6423904 6432723 a 0 - 4 4 chrY 2909080 2911300 a 0 - 5 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7448040 | 7453318 | a | 0 | - | | chr1 | 7396910 | 7398152 | a | 0 | - | | chr1 | 7749391 | 7752779 | a | 0 | - | | chr4 | 6423904 | 6432723 | a | 0 | - | | chrY | 2909080 | 2911300 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr2 | 6682511 | 6687370 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpbfpjjpx3/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr2 6682511 6687370 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr2 | 6682511 | 6687370 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4538370 | 4544417 | a | 0 | + | | chr1 | 5366836 | 5373511 | a | 0 | - | | chr4 | 6212017 | 6213910 | a | 0 | + | | chr16 | 6517843 | 6526855 | a | 0 | - | | chrY | 6205350 | 6209471 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpp8gh4no1/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 4538370 4544417 a 0 + 1 1 chr1 5366836 5373511 a 0 - 2 2 chr16 6517843 6526855 a 0 - 3 3 chr4 6212017 6213910 a 0 + 4 4 chrY 6205350 6209471 a 0 + 5 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4538370 | 4544417 | a | 0 | + | | chr1 | 5366836 | 5373511 | a | 0 | - | | chr4 | 6212017 | 6213910 | a | 0 | + | | chr16 | 6517843 | 6526855 | a | 0 | - | | chrY | 6205350 | 6209471 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1213540 | 1222165 | a | 0 | + | | chr1 | 7767184 | 7775809 | a | 0 | - | | chr8 | 8747440 | 8756065 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp5ts58p44/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1213540 1222165 a 0 + 1 1 chr1 7767184 7775809 a 0 - 2 2 chr8 8747440 8756065 a 0 - 3 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1213540 | 1222165 | a | 0 | + | | chr1 | 7767184 | 7775809 | a | 0 | - | | chr8 | 8747440 | 8756065 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3949519 | 3953465 | a | 0 | + | | chr1 | 946021 | 955556 | a | 0 | - | | chr3 | 3414358 | 3415560 | a | 0 | - | | chr4 | 6142148 | 6148704 | a | 0 | - | | chr4 | 3700445 | 3701375 | a | 0 | - | | chr4 | 429631 | 438651 | a | 0 | - | | chr4 | 4315747 | 4318039 | a | 0 | - | | chr8 | 4028782 | 4038782 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 8 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp1ug5vcu_/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 946021 955556 a 0 - 1 1 chr1 3949519 3953465 a 0 + 2 2 chr3 3414358 3415560 a 0 - 3 3 chr4 429631 438651 a 0 - 4 4 chr4 3700445 3701375 a 0 - 5 5 chr4 4315747 4318039 a 0 - 6 6 chr4 6142148 6148704 a 0 - 7 7 chr8 4028782 4038782 a 0 - 8 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3949519 | 3953465 | a | 0 | + | | chr1 | 946021 | 955556 | a | 0 | - | | chr3 | 3414358 | 3415560 | a | 0 | - | | chr4 | 6142148 | 6148704 | a | 0 | - | | chr4 | 3700445 | 3701375 | a | 0 | - | | chr4 | 429631 | 438651 | a | 0 | - | | chr4 | 4315747 | 4318039 | a | 0 | - | | chr8 | 4028782 | 4038782 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 8 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3889773 | 3893163 | a | 0 | + | | chr8 | 7302040 | 7309315 | a | 0 | + | | chr9 | 4670963 | 4676677 | a | 0 | + | | chr11 | 3404281 | 3406677 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr16 | 4755088 | 4760098 | a | 0 | + | | chr16 | 8915126 | 8915990 | a | 0 | + | | chr20 | 957528 | 966180 | a | 0 | + | | chrY | 4704792 | 4714755 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 9 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmppsxwbx78/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 3889773 3893163 a 0 + 1 1 chr11 3404281 3406677 a 0 + 2 2 chr13 3880516 3885278 a 0 + 3 3 chr15 4483864 4488797 a 0 + 4 4 chr16 4755088 4760098 a 0 + 5 5 chr16 8915126 8915990 a 0 + 6 6 chr20 957528 966180 a 0 + 7 7 chr8 7302040 7309315 a 0 + 8 8 chr9 4670963 4676677 a 0 + 9 9 chrY 4704792 4714755 a 0 + 10 10 chrY 9078045 9088045 a 0 + 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3889773 | 3893163 | a | 0 | + | | chr8 | 7302040 | 7309315 | a | 0 | + | | chr9 | 4670963 | 4676677 | a | 0 | + | | chr11 | 3404281 | 3406677 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr16 | 4755088 | 4760098 | a | 0 | + | | chr16 | 8915126 | 8915990 | a | 0 | + | | chr20 | 957528 | 966180 | a | 0 | + | | chrY | 4704792 | 4714755 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 9 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 253621 | 263621 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpoa33vlra/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 253621 263621 a 0 - 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 253621 | 263621 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9922308 | 9932308 | a | 0 | + | | chr15 | 3193297 | 3193299 | a | 0 | + | | chr20 | 2749392 | 2754554 | a | 0 | - | | chr22 | 3753286 | 3759611 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpg56qd1lh/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 9922308 9932308 a 0 + 1 1 chr15 3193297 3193299 a 0 + 2 2 chr20 2749392 2754554 a 0 - 3 3 chr22 3753286 3759611 a 0 + 4 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9922308 | 9932308 | a | 0 | + | | chr15 | 3193297 | 3193299 | a | 0 | + | | chr20 | 2749392 | 2754554 | a | 0 | - | | chr22 | 3753286 | 3759611 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8463722 | 8464164 | a | 0 | - | | chr1 | 1578945 | 1587291 | a | 0 | - | | chr1 | 2173121 | 2176075 | a | 0 | - | | chr17 | 4696432 | 4698401 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpky4cms4y/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1578945 1587291 a 0 - 1 1 chr1 2173121 2176075 a 0 - 2 2 chr1 8463722 8464164 a 0 - 3 3 chr17 4696432 4698401 a 0 - 4 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8463722 | 8464164 | a | 0 | - | | chr1 | 1578945 | 1587291 | a | 0 | - | | chr1 | 2173121 | 2176075 | a | 0 | - | | chr17 | 4696432 | 4698401 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7377086 | 7380742 | a | 0 | + | | chr1 | 7681160 | 7688824 | a | 0 | - | | chr1 | 2775061 | 2781895 | a | 0 | - | | chr1 | 1722799 | 1732413 | a | 0 | - | | chr12 | 10000000 | 10005364 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpkvl8uoln/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1722799 1732413 a 0 - 1 1 chr1 2775061 2781895 a 0 - 2 2 chr1 7377086 7380742 a 0 + 3 3 chr1 7681160 7688824 a 0 - 4 4 chr12 10000000 10005364 a 0 - 5 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7377086 | 7380742 | a | 0 | + | | chr1 | 7681160 | 7688824 | a | 0 | - | | chr1 | 2775061 | 2781895 | a | 0 | - | | chr1 | 1722799 | 1732413 | a | 0 | - | | chr12 | 10000000 | 10005364 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chrY | 5490241 | 5496125 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmps38rhc_7/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chrY 5490241 5496125 a 0 - 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chrY | 5490241 | 5496125 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2673055 | 2682794 | a | 0 | - | | chr1 | 4613620 | 4617105 | a | 0 | - | | chr1 | 9363544 | 9370746 | a | 0 | - | | chr1 | 9322840 | 9322842 | a | 0 | - | | chr1 | 9647050 | 9651223 | a | 0 | - | | chr1 | 6176643 | 6183845 | a | 0 | - | | chr1 | 2866131 | 2873517 | a | 0 | - | | chr9 | 1859029 | 1860955 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 8 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp410ibp85/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2673055 2682794 a 0 - 1 1 chr1 2866131 2873517 a 0 - 2 2 chr1 4613620 4617105 a 0 - 3 3 chr1 6176643 6183845 a 0 - 4 4 chr1 9322840 9322842 a 0 - 5 5 chr1 9363544 9370746 a 0 - 6 6 chr1 9647050 9651223 a 0 - 7 7 chr9 1859029 1860955 a 0 - 8 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2673055 | 2682794 | a | 0 | - | | chr1 | 4613620 | 4617105 | a | 0 | - | | chr1 | 9363544 | 9370746 | a | 0 | - | | chr1 | 9322840 | 9322842 | a | 0 | - | | chr1 | 9647050 | 9651223 | a | 0 | - | | chr1 | 6176643 | 6183845 | a | 0 | - | | chr1 | 2866131 | 2873517 | a | 0 | - | | chr9 | 1859029 | 1860955 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 8 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr13 | 7326554 | 7332668 | a | 0 | - | | chr15 | 5848119 | 5854564 | a | 0 | - | | chr20 | 3069529 | 3073686 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp91wxxqd_/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr13 7326554 7332668 a 0 - 1 1 chr15 5848119 5854564 a 0 - 2 2 chr20 3069529 3073686 a 0 - 3 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr13 | 7326554 | 7332668 | a | 0 | - | | chr15 | 5848119 | 5854564 | a | 0 | - | | chr20 | 3069529 | 3073686 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8402738 | 8410237 | a | 0 | + | | chr1 | 929192 | 931806 | a | 0 | + | | chr1 | 3661745 | 3669244 | a | 0 | - | | chr1 | 10000000 | 10001048 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr10 | 1019953 | 1024146 | a | 0 | + | | chr10 | 2363862 | 2373703 | a | 0 | - | | chr17 | 7029786 | 7036968 | a | 0 | + | | chr18 | 7029786 | 7037285 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 10 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpqvefht5w/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 929192 931806 a 0 + 1 1 chr1 3661745 3669244 a 0 - 2 2 chr1 8402738 8410237 a 0 + 3 3 chr1 10000000 10001048 a 0 - 4 4 chr10 1019953 1024146 a 0 + 5 5 chr10 2363862 2373703 a 0 - 6 6 chr17 7029786 7036968 a 0 + 7 7 chr18 7029786 7037285 a 0 - 8 8 chr19 4205477 4212976 a 0 - 9 9 chr4 773262 780761 a 0 + 10 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8402738 | 8410237 | a | 0 | + | | chr1 | 929192 | 931806 | a | 0 | + | | chr1 | 3661745 | 3669244 | a | 0 | - | | chr1 | 10000000 | 10001048 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr10 | 1019953 | 1024146 | a | 0 | + | | chr10 | 2363862 | 2373703 | a | 0 | - | | chr17 | 7029786 | 7036968 | a | 0 | + | | chr18 | 7029786 | 7037285 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 10 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8525066 | 8532328 | a | 0 | + | | chr1 | 7693832 | 7699625 | a | 0 | + | | chr1 | 2430864 | 2436265 | a | 0 | + | | chr1 | 1938487 | 1938650 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr1 | 3716158 | 3718123 | a | 0 | - | | chr1 | 8525066 | 8529490 | a | 0 | - | | chr1 | 2578475 | 2578511 | a | 0 | - | | chr1 | 7352286 | 7361931 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp2391cmyj/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1938487 1938650 a 0 - 1 1 chr1 2430864 2436265 a 0 + 2 2 chr1 2578475 2578511 a 0 - 3 3 chr1 3716158 3718123 a 0 - 4 4 chr1 7352286 7361931 a 0 - 5 5 chr1 7693832 7699625 a 0 + 6 6 chr1 8525066 8529490 a 0 - 7 7 chr1 8525066 8532328 a 0 + 7 8 chr17 666364 670708 a 0 + 8 9 chr18 8525066 8526803 a 0 + 9 10 chrY 5081799 5086007 a 0 - 10 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8525066 | 8532328 | a | 0 | + | | chr1 | 7693832 | 7699625 | a | 0 | + | | chr1 | 2430864 | 2436265 | a | 0 | + | | chr1 | 1938487 | 1938650 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr1 | 3716158 | 3718123 | a | 0 | - | | chr1 | 8525066 | 8529490 | a | 0 | - | | chr1 | 2578475 | 2578511 | a | 0 | - | | chr1 | 7352286 | 7361931 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1593985 | 1603556 | a | 0 | - | | chr2 | 7491017 | 7491250 | a | 0 | + | | chr13 | 1593985 | 1594218 | a | 0 | - | | chr15 | 7833445 | 7834658 | a | 0 | - | | chr18 | 402477 | 406577 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpyqve6j7h/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1593985 1603556 a 0 - 1 1 chr13 1593985 1594218 a 0 - 2 2 chr15 7833445 7834658 a 0 - 3 3 chr18 402477 406577 a 0 - 4 4 chr2 7491017 7491250 a 0 + 5 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1593985 | 1603556 | a | 0 | - | | chr2 | 7491017 | 7491250 | a | 0 | + | | chr13 | 1593985 | 1594218 | a | 0 | - | | chr15 | 7833445 | 7834658 | a | 0 | - | | chr18 | 402477 | 406577 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1530647 | 1533276 | a | 0 | + | | chr1 | 8482880 | 8488024 | a | 0 | + | | chr1 | 9994427 | 9999180 | a | 0 | - | | chr1 | 5591930 | 5597036 | a | 0 | - | | chr1 | 6312706 | 6319725 | a | 0 | - | | chr1 | 7577318 | 7580336 | a | 0 | - | | chr7 | 4745659 | 4754154 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 7 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpw4am3iq7/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1530647 1533276 a 0 + 1 1 chr1 5591930 5597036 a 0 - 2 2 chr1 6312706 6319725 a 0 - 3 3 chr1 7577318 7580336 a 0 - 4 4 chr1 8482880 8488024 a 0 + 5 5 chr1 9994427 9999180 a 0 - 6 6 chr7 4745659 4754154 a 0 - 7 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1530647 | 1533276 | a | 0 | + | | chr1 | 8482880 | 8488024 | a | 0 | + | | chr1 | 9994427 | 9999180 | a | 0 | - | | chr1 | 5591930 | 5597036 | a | 0 | - | | chr1 | 6312706 | 6319725 | a | 0 | - | | chr1 | 7577318 | 7580336 | a | 0 | - | | chr7 | 4745659 | 4754154 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 7 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2779018 | 2781641 | a | 0 | + | | chr1 | 1265502 | 1273526 | a | 0 | - | | chr20 | 7650431 | 7656440 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp0leusxrp/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1265502 1273526 a 0 - 1 1 chr1 2779018 2781641 a 0 + 2 2 chr20 7650431 7656440 a 0 - 3 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2779018 | 2781641 | a | 0 | + | | chr1 | 1265502 | 1273526 | a | 0 | - | | chr20 | 7650431 | 7656440 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5326204 | 5334713 | a | 0 | + | | chr1 | 3452147 | 3455980 | a | 0 | + | | chr1 | 7829871 | 7835327 | a | 0 | - | | chr1 | 1731047 | 1736308 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr8 | 2068709 | 2078313 | a | 0 | - | | chr12 | 5486486 | 5493583 | a | 0 | + | | chr14 | 4202689 | 4205998 | a | 0 | - | | chr14 | 1038946 | 1043263 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 9 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmph25ee7jh/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1731047 1736308 a 0 - 1 1 chr1 3452147 3455980 a 0 + 2 2 chr1 5326204 5334713 a 0 + 3 3 chr1 7829871 7835327 a 0 - 4 4 chr12 5486486 5493583 a 0 + 5 5 chr14 1038946 1043263 a 0 - 6 6 chr14 4202689 4205998 a 0 - 7 7 chr2 1473060 1478146 a 0 + 8 8 chr8 2068709 2078313 a 0 - 9 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5326204 | 5334713 | a | 0 | + | | chr1 | 3452147 | 3455980 | a | 0 | + | | chr1 | 7829871 | 7835327 | a | 0 | - | | chr1 | 1731047 | 1736308 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr8 | 2068709 | 2078313 | a | 0 | - | | chr12 | 5486486 | 5493583 | a | 0 | + | | chr14 | 4202689 | 4205998 | a | 0 | - | | chr14 | 1038946 | 1043263 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 9 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4313983 | 4321095 | a | 0 | - | | chr6 | 7714327 | 7721337 | a | 0 | + | | chr20 | 4313983 | 4315790 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpq296cham/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 4313983 4321095 a 0 - 1 1 chr20 4313983 4315790 a 0 - 2 2 chr6 7714327 7721337 a 0 + 3 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4313983 | 4321095 | a | 0 | - | | chr6 | 7714327 | 7721337 | a | 0 | + | | chr20 | 4313983 | 4315790 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7963173 | 7967518 | a | 0 | - | | chr1 | 1 | 2104 | a | 0 | - | | chr6 | 8620678 | 8624120 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp42l4ffsd/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 2104 a 0 - 1 1 chr1 7963173 7967518 a 0 - 2 2 chr6 8620678 8624120 a 0 - 3 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7963173 | 7967518 | a | 0 | - | | chr1 | 1 | 2104 | a | 0 | - | | chr6 | 8620678 | 8624120 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 4996 | a | 0 | + | | chr1 | 1063613 | 1070697 | a | 0 | + | | chr1 | 3233900 | 3235402 | a | 0 | - | | chr1 | 443235 | 450963 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr11 | 6319278 | 6322748 | a | 0 | - | | chr13 | 8677046 | 8679644 | a | 0 | + | | chr13 | 1817794 | 1827316 | a | 0 | - | | chrY | 1391681 | 1397594 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp6upd4t_z/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 4996 a 0 + 1 1 chr1 443235 450963 a 0 - 2 2 chr1 1063613 1070697 a 0 + 3 3 chr1 3233900 3235402 a 0 - 4 4 chr1 3659071 3659073 a 0 - 5 5 chr1 4960522 4963094 a 0 - 6 6 chr11 6319278 6322748 a 0 - 7 7 chr13 1817794 1827316 a 0 - 8 8 chr13 8677046 8679644 a 0 + 9 9 chr9 6937864 6942845 a 0 + 10 10 chrY 1391681 1397594 a 0 - 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 4996 | a | 0 | + | | chr1 | 1063613 | 1070697 | a | 0 | + | | chr1 | 3233900 | 3235402 | a | 0 | - | | chr1 | 443235 | 450963 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr11 | 6319278 | 6322748 | a | 0 | - | | chr13 | 8677046 | 8679644 | a | 0 | + | | chr13 | 1817794 | 1827316 | a | 0 | - | | chrY | 1391681 | 1397594 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9434241 | 9441897 | a | 0 | - | | chr14 | 6584539 | 6585828 | a | 0 | - | | chr14 | 9782777 | 9792178 | a | 0 | - | | chr19 | 362515 | 364417 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpw8ny41by/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 9434241 9441897 a 0 - 1 1 chr14 6584539 6585828 a 0 - 2 2 chr14 9782777 9792178 a 0 - 3 3 chr19 362515 364417 a 0 - 4 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9434241 | 9441897 | a | 0 | - | | chr14 | 6584539 | 6585828 | a | 0 | - | | chr14 | 9782777 | 9792178 | a | 0 | - | | chr19 | 362515 | 364417 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2567339 | 2576218 | a | 0 | + | | chr1 | 2567339 | 2573081 | a | 0 | - | | chr1 | 2567339 | 2570188 | a | 0 | - | | chr1 | 2567339 | 2568948 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr7 | 2567339 | 2573355 | a | 0 | + | | chr16 | 2567339 | 2575560 | a | 0 | - | | chr17 | 2567339 | 2568768 | a | 0 | - | | chrY | 2567339 | 2573052 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 10 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpxf8xqbgb/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2567339 2568948 a 0 - 1 1 chr1 2567339 2570188 a 0 - 1 2 chr1 2567339 2573081 a 0 - 1 3 chr1 2567339 2573656 a 0 - 1 4 chr1 2567339 2573989 a 0 - 1 5 chr1 2567339 2576218 a 0 + 1 6 chr16 2567339 2575560 a 0 - 2 7 chr17 2567339 2568768 a 0 - 3 8 chr7 2567339 2573355 a 0 + 4 9 chrY 2567339 2573052 a 0 + 5 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2567339 | 2576218 | a | 0 | + | | chr1 | 2567339 | 2573081 | a | 0 | - | | chr1 | 2567339 | 2570188 | a | 0 | - | | chr1 | 2567339 | 2568948 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr7 | 2567339 | 2573355 | a | 0 | + | | chr16 | 2567339 | 2575560 | a | 0 | - | | chr17 | 2567339 | 2568768 | a | 0 | - | | chrY | 2567339 | 2573052 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 10 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7061810 | 7071137 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpb4ml53yd/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 7061810 7071137 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7061810 | 7071137 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1888845 | 1898019 | a | 0 | + | | chr1 | 1 | 3127 | a | 0 | + | | chr1 | 6106973 | 6107362 | a | 0 | + | | chr1 | 8330726 | 8339988 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chrX | 3954874 | 3957255 | a | 0 | + | | chrX | 532412 | 536962 | a | 0 | + | | chrX | 7016111 | 7016112 | a | 0 | - | | chrX | 8330726 | 8340726 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpks_7eo2g/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 3127 a 0 + 1 1 chr1 1888845 1898019 a 0 + 2 2 chr1 6106973 6107362 a 0 + 3 3 chr1 8330726 8339988 a 0 - 4 4 chr10 7496502 7499122 a 0 - 5 5 chrM 8330726 8337548 a 0 - 6 6 chrX 532412 536962 a 0 + 7 7 chrX 3954874 3957255 a 0 + 8 8 chrX 7016111 7016112 a 0 - 9 9 chrX 8330726 8340726 a 0 - 10 10 chrY 1240193 1247208 a 0 - 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1888845 | 1898019 | a | 0 | + | | chr1 | 1 | 3127 | a | 0 | + | | chr1 | 6106973 | 6107362 | a | 0 | + | | chr1 | 8330726 | 8339988 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chrX | 3954874 | 3957255 | a | 0 | + | | chrX | 532412 | 536962 | a | 0 | + | | chrX | 7016111 | 7016112 | a | 0 | - | | chrX | 8330726 | 8340726 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6133193 | 6135859 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpi59r42en/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 6133193 6135859 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6133193 | 6135859 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4649255 | 4649499 | a | 0 | + | | chr1 | 6484584 | 6492740 | a | 0 | + | | chr1 | 9356709 | 9360244 | a | 0 | + | | chr1 | 5238759 | 5247347 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr17 | 6504537 | 6512937 | a | 0 | + | | chr20 | 2276069 | 2285547 | a | 0 | + | | chr20 | 3180951 | 3185812 | a | 0 | + | | chrY | 587258 | 594408 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpf_kvb875/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 3351 a 0 - 1 1 chr1 3704560 3705652 a 0 + 2 2 chr1 4649255 4649499 a 0 + 3 3 chr1 5238759 5247347 a 0 + 4 4 chr1 6484584 6492740 a 0 + 5 5 chr1 9356709 9360244 a 0 + 6 6 chr17 6504537 6512937 a 0 + 7 7 chr20 2276069 2285547 a 0 + 8 8 chr20 3180951 3185812 a 0 + 9 9 chr4 9836534 9842533 a 0 + 10 10 chrY 587258 594408 a 0 - 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4649255 | 4649499 | a | 0 | + | | chr1 | 6484584 | 6492740 | a | 0 | + | | chr1 | 9356709 | 9360244 | a | 0 | + | | chr1 | 5238759 | 5247347 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr17 | 6504537 | 6512937 | a | 0 | + | | chr20 | 2276069 | 2285547 | a | 0 | + | | chr20 | 3180951 | 3185812 | a | 0 | + | | chrY | 587258 | 594408 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1985831 | 1987854 | a | 0 | + | | chr3 | 9826299 | 9828322 | a | 0 | + | | chr3 | 9999999 | 10002022 | a | 0 | + | | chr3 | 5385318 | 5387341 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr3 | 7992165 | 7994188 | a | 0 | + | | chr3 | 7982043 | 7984066 | a | 0 | + | | chr3 | 7977675 | 7979698 | a | 0 | - | | chr3 | 5561343 | 5563366 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpjmve9n0t/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1985831 1987854 a 0 + 1 1 chr3 1553084 1555107 a 0 + 2 2 chr3 1863908 1865931 a 0 + 3 3 chr3 3143265 3145288 a 0 + 4 4 chr3 5385318 5387341 a 0 + 5 5 chr3 5561343 5563366 a 0 - 6 6 chr3 7977675 7979698 a 0 - 7 7 chr3 7982043 7984066 a 0 + 8 8 chr3 7992165 7994188 a 0 + 9 9 chr3 9826299 9828322 a 0 + 10 10 chr3 9999999 10002022 a 0 + 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1985831 | 1987854 | a | 0 | + | | chr3 | 9826299 | 9828322 | a | 0 | + | | chr3 | 9999999 | 10002022 | a | 0 | + | | chr3 | 5385318 | 5387341 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr3 | 7992165 | 7994188 | a | 0 | + | | chr3 | 7982043 | 7984066 | a | 0 | + | | chr3 | 7977675 | 7979698 | a | 0 | - | | chr3 | 5561343 | 5563366 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9976379 | 9984497 | a | 0 | + | | chr1 | 9976379 | 9983492 | a | 0 | + | | chr1 | 9976379 | 9984713 | a | 0 | + | | chr1 | 9976379 | 9985935 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr17 | 9976379 | 9978966 | a | 0 | + | | chr18 | 9976379 | 9980660 | a | 0 | + | | chrX | 9976379 | 9976633 | a | 0 | + | | chrX | 9976379 | 9986010 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp2hgmj1un/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 9976379 9976526 a 0 - 1 1 chr1 9976379 9983492 a 0 + 1 2 chr1 9976379 9984497 a 0 + 1 3 chr1 9976379 9984713 a 0 + 1 4 chr1 9976379 9985168 a 0 - 1 5 chr1 9976379 9985935 a 0 - 1 6 chr17 9976379 9978966 a 0 + 2 7 chr18 9976379 9980660 a 0 + 3 8 chr3 9976379 9985970 a 0 + 4 9 chrX 9976379 9976633 a 0 + 5 10 chrX 9976379 9986010 a 0 - 5 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9976379 | 9984497 | a | 0 | + | | chr1 | 9976379 | 9983492 | a | 0 | + | | chr1 | 9976379 | 9984713 | a | 0 | + | | chr1 | 9976379 | 9985935 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr17 | 9976379 | 9978966 | a | 0 | + | | chr18 | 9976379 | 9980660 | a | 0 | + | | chrX | 9976379 | 9976633 | a | 0 | + | | chrX | 9976379 | 9986010 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpuipfm7c3/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 2 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. _________________________________ test_summary _________________________________ [gw1] linux -- Python 3.12.6 /usr/bin/python3.12 @pytest.mark.bedtools > @settings( max_examples=max_examples, deadline=deadline, print_blob=True, suppress_health_check=HealthCheck.all()) tests/test_unary.py:311: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_unary.py:322: in test_summary gr.summary() pyranges/pyranges.py:4475: in summary return _summary(self, to_stdout, return_df) pyranges/methods/summary.py:16: in _summary c = self.merge(strand=True) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_summary( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., # or any other generated value E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicY2TABAAAKAAC') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- {'Chromosome': ['chr1'], 'Start': [1], 'End': [2], 'Name': ['a'], 'Score': [0], 'Strand': ['+']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr2', 'chr5', 'chr5', 'chr9', 'chr9', 'chr21'], 'Start': [8781811, 5361272, 7368522, 1652850, 9668378, 2589118, 3022493, 2139274, 1652850, 3940841], 'End': [8789250, 5362951, 7377119, 1662849, 9677991, 2592982, 3024416, 2140417, 1654373, 3947478], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0, 0, 0, 0], 'Strand': ['+', '+', '-', '-', '-', '+', '+', '-', '-', '-']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr4', 'chr5', 'chr5', 'chr9', 'chr21'], 'Start': [5361272, 8781811, 1, 8, 65537, 10000000, 2589118, 3022493, 2, 3940841], 'End': [5362951, 8788268, 258, 1151, 75536, 10008253, 2589123, 3024416, 1525, 3940842], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0, 0, 0, 0], 'Strand': ['+', '-', '-', '-', '-', '+', '-', '-', '-', '-']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr4', 'chr5', 'chr5', 'chr9', 'chr21'], 'Start': [1, 5361272, 8781811, 8, 65537, 10000000, 2589118, 3022493, 2, 3940841], 'End': [258, 5362951, 8788268, 1151, 75536, 10008253, 2589123, 3024416, 1525, 3940842], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0, 0, 0, 0], 'Strand': ['+', '+', '-', '-', '-', '+', '-', '-', '-', '-']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr4', 'chr5', 'chr5', 'chr9', 'chr21'], 'Start': [8781811, 8, 65537, 1, 5361272, 10000000, 2589118, 3022493, 2, 3940841], 'End': [8788268, 1151, 75536, 258, 5362951, 10008253, 2589123, 3024416, 1525, 3940842], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0, 0, 0, 0], 'Strand': ['+', '+', '+', '-', '-', '+', '+', '+', '+', '+']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr4', 'chr5', 'chr5', 'chr9', 'chr21'], 'Start': [8781811, 8, 65537, 1, 5361272, 10000000, 2589118, 3022493, 2, 3940841], 'End': [8783347, 16, 65794, 2, 5365831, 10010000, 2589119, 3029662, 4, 3940842], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0, 0, 0, 0], 'Strand': ['+', '+', '+', '-', '-', '+', '+', '+', '+', '+']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr5', 'chr9', 'chr21'], 'Start': [65537, 65537, 65537, 65537, 65537, 65537, 65537, 9, 6], 'End': [65794, 65541, 65541, 65541, 65541, 65538, 65541, 13, 10], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0, 0, 0], 'Strand': ['+', '+', '+', '+', '+', '-', '+', '+', '+']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr5', 'chr9', 'chr21'], 'Start': [65537, 65537, 65537, 65537, 65537, 65537, 65537, 9, 6], 'End': [65794, 65538, 65794, 65794, 65794, 65540, 65794, 266, 263], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0, 0, 0], 'Strand': ['-', '-', '-', '-', '-', '-', '-', '-', '-']} {'Chromosome': ['chr1', 'chr21', 'chrM'], 'Start': [9012798, 6345295, 5619946], 'End': [9016008, 6347653, 5625270], 'Name': ['a', 'a', 'a'], 'Score': [0, 0, 0], 'Strand': ['+', '-', '+']} {'Chromosome': ['chr1', 'chr21', 'chrM'], 'Start': [9012798, 6345295, 5619946], 'End': [9016008, 6347653, 5625270], 'Name': ['a', 'a', 'a'], 'Score': [0, 0, 0], 'Strand': ['+', '-', '+']} {'Chromosome': ['chr1'], 'Start': [1], 'End': [2], 'Name': ['a'], 'Score': [0], 'Strand': ['+']} {'Chromosome': ['chr1'], 'Start': [1], 'End': [2], 'Name': ['a'], 'Score': [0], 'Strand': ['+']} {'Chromosome': ['chr1'], 'Start': [1], 'End': [2], 'Name': ['a'], 'Score': [0], 'Strand': ['+']} {'Chromosome': ['chr1'], 'Start': [1], 'End': [2], 'Name': ['a'], 'Score': [0], 'Strand': ['-']} {'Chromosome': ['chr1'], 'Start': [1], 'End': [2], 'Name': ['a'], 'Score': [0], 'Strand': ['-']} {'Chromosome': ['chr1', 'chr1', 'chr16'], 'Start': [5214400, 4325297, 7268944], 'End': [5217051, 4326504, 7270151], 'Name': ['a', 'a', 'a'], 'Score': [0, 0, 0], 'Strand': ['-', '-', '-']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr2', 'chr4', 'chr22'], 'Start': [2762647, 5697180, 3000282, 8287185, 5233749, 2982792, 7714453, 1916773, 727295, 6093519], 'End': [2769731, 5704164, 3006926, 8288473, 5234957, 2982793, 7721355, 1925183, 728718, 6096759], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0, 0, 0, 0], 'Strand': ['+', '+', '+', '+', '-', '-', '-', '-', '+', '-']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr3', 'chr12'], 'Start': [6472147, 6111901, 6186856, 3946479, 7341075, 7236794, 4064073, 1522064], 'End': [6478040, 6114938, 6190856, 3947804, 7346014, 7241647, 4067690, 1527228], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0, 0], 'Strand': ['+', '+', '-', '-', '-', '-', '-', '+']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr7', 'chr11', 'chr11', 'chr22'], 'Start': [8865434, 1842574, 7176077, 7741970, 9822149, 9532167, 4456945], 'End': [8874010, 1842850, 7182899, 7750574, 9822552, 9540221, 4465103], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0], 'Strand': ['+', '+', '-', '+', '+', '+', '-']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr8', 'chr11', 'chr12', 'chrM'], 'Start': [2140864, 2209437, 3851418, 5549764, 342674, 8643862, 73572, 1004058, 5120460, 4868900], 'End': [2144665, 2213084, 3859393, 5553148, 346058, 8651088, 82058, 1008729, 5122333, 4877269], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0, 0, 0, 0], 'Strand': ['+', '+', '-', '-', '-', '-', '+', '+', '+', '+']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr14', 'chr19', 'chr19', 'chr21', 'chr22'], 'Start': [7099678, 3651169, 7561925, 3919084, 9907617, 4734392, 7869034, 152123, 7735438], 'End': [7099848, 3651339, 7569482, 3921923, 9908334, 4739586, 7875875, 152293, 7745276], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0, 0, 0], 'Strand': ['+', '+', '-', '-', '-', '+', '-', '+', '+']} {'Chromosome': ['chr1', 'chr1', 'chr7', 'chr7', 'chr10', 'chr12', 'chr18', 'chr22', 'chr22'], 'Start': [1305126, 6959913, 3721999, 290412, 8876017, 9507904, 7547588, 9507904, 9507904], 'End': [1309610, 6961776, 3722406, 299340, 8882166, 9510959, 7554083, 9513412, 9515697], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0, 0, 0], 'Strand': ['+', '+', '+', '+', '+', '+', '-', '+', '-']} {'Chromosome': ['chr1', 'chr6', 'chr9', 'chr9', 'chr9', 'chr14', 'chr22'], 'Start': [2615422, 5354887, 4538400, 5614356, 1749158, 4999618, 2285388], 'End': [2619018, 5355165, 4547354, 5620364, 1749584, 5006582, 2285406], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0], 'Strand': ['+', '+', '+', '+', '-', '+', '-']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr5'], 'Start': [3498711, 3944608, 9015717, 3445183, 653166, 2710764], 'End': [3503526, 3949423, 9020532, 3455182, 656090, 2718234], 'Name': ['a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0], 'Strand': ['-', '-', '-', '-', '-', '+']} {'Chromosome': ['chr1', 'chr5', 'chr9', 'chr9', 'chrY'], 'Start': [1547664, 2351435, 3125745, 3680640, 4606671], 'End': [1550997, 2353371, 3132932, 3684957, 4610071], 'Name': ['a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0], 'Strand': ['-', '-', '-', '-', '-']} {'Chromosome': ['chr1', 'chr1', 'chr18'], 'Start': [1557655, 7281963, 2334967], 'End': [1560286, 7289541, 2339954], 'Name': ['a', 'a', 'a'], 'Score': [0, 0, 0], 'Strand': ['-', '-', '-']} {'Chromosome': ['chr1'], 'Start': [8561694], 'End': [8564173], 'Name': ['a'], 'Score': [0], 'Strand': ['+']} {'Chromosome': ['chr1', 'chr2', 'chr8'], 'Start': [2380148, 9329281, 9523316], 'End': [2382227, 9337547, 9532930], 'Name': ['a', 'a', 'a'], 'Score': [0, 0, 0], 'Strand': ['-', '-', '-']} {'Chromosome': ['chr4'], 'Start': [1], 'End': [64], 'Name': ['a'], 'Score': [0], 'Strand': ['+']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr5', 'chr6', 'chr6', 'chr14', 'chrX'], 'Start': [45761, 699065, 699065, 699065, 5710451, 699065, 4691117, 4139390, 699065, 699065], 'End': [51086, 699464, 702805, 708820, 5720084, 701455, 4696686, 4148126, 700728, 699066], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0, 0, 0, 0], 'Strand': ['+', '+', '+', '-', '-', '-', '+', '-', '+', '-']} {'Chromosome': ['chr4', 'chr12'], 'Start': [8570994, 5744143], 'End': [8577320, 5752264], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['-', '-']} {'Chromosome': ['chr5'], 'Start': [30862], 'End': [35997], 'Name': ['a'], 'Score': [0], 'Strand': ['-']} {'Chromosome': ['chr1', 'chr1'], 'Start': [10000000, 8307617], 'End': [10005307, 8317183], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['+', '-']} {'Chromosome': ['chr1'], 'Start': [6494647], 'End': [6496115], 'Name': ['a'], 'Score': [0], 'Strand': ['-']} {'Chromosome': ['chr1', 'chr1'], 'Start': [8623315, 6394797], 'End': [8631524, 6404797], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['+', '-']} {'Chromosome': ['chr1', 'chr8', 'chr16'], 'Start': [4943299, 4624020, 725607], 'End': [4953299, 4626144, 727257], 'Name': ['a', 'a', 'a'], 'Score': [0, 0, 0], 'Strand': ['+', '-', '-']} {'Chromosome': ['chr1', 'chr6'], 'Start': [3043880, 6196649], 'End': [3047078, 6205917], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['-', '-']} {'Chromosome': ['chr1', 'chr9'], 'Start': [3523102, 7921745], 'End': [3529641, 7927422], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['+', '+']} {'Chromosome': ['chr1', 'chr1'], 'Start': [4965731, 9169751], 'End': [4968690, 9172018], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['+', '-']} {'Chromosome': ['chr1', 'chr1', 'chr7', 'chr12', 'chr14', 'chr14', 'chr14', 'chr17', 'chrY'], 'Start': [2263153, 10000000, 7382036, 5688676, 5904077, 344330, 1632192, 611552, 6055788], 'End': [2267685, 10003204, 7386680, 5692539, 5914077, 349702, 1635744, 615541, 6056788], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0, 0, 0], 'Strand': ['+', '-', '+', '+', '+', '+', '-', '-', '-']} {'Chromosome': ['chr1'], 'Start': [2], 'End': [1780], 'Name': ['a'], 'Score': [0], 'Strand': ['+']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr9', 'chr11', 'chr19', 'chrM', 'chrX'], 'Start': [7039720, 5797646, 9272648, 9017293, 7456541, 6072913, 1062579, 4486281, 8140221, 6719372], 'End': [7040264, 5798190, 9273192, 9017837, 7457085, 6081527, 1063123, 4490716, 8145507, 6719916], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0, 0, 0, 0], 'Strand': ['+', '+', '-', '-', '-', '-', '-', '-', '-', '-']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr8', 'chr8', 'chr14', 'chr14', 'chr14', 'chr15'], 'Start': [1, 9399360, 889321, 8128089, 9310091, 802077, 8635774, 8785057, 1843060, 8398192], 'End': [8681, 9401219, 890540, 8136359, 9313574, 811297, 8636937, 8786276, 1846343, 8405111], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0, 0, 0, 0], 'Strand': ['+', '+', '-', '-', '+', '+', '+', '+', '-', '+']} {'Chromosome': ['chr1', 'chr14', 'chr15', 'chr16'], 'Start': [7850552, 8084581, 8084581, 9269227], 'End': [7851469, 8091712, 8093052, 9278145], 'Name': ['a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0], 'Strand': ['+', '+', '+', '+']} {'Chromosome': ['chr1', 'chr1'], 'Start': [9924194, 1975650], 'End': [9932810, 1980273], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['+', '-']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr2', 'chr11', 'chr13', 'chr19', 'chr20', 'chrY'], 'Start': [6658544, 1285698, 61368, 8295204, 1287355, 9194803, 9953498, 3433733, 3531346, 7559550], 'End': [6666535, 1293167, 68473, 8305203, 1294585, 9195866, 9962614, 3437960, 3536453, 7563633], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0, 0, 0, 0], 'Strand': ['+', '+', '-', '-', '+', '+', '+', '+', '-', '+']} {'Chromosome': ['chr13'], 'Start': [1114988], 'End': [1117411], 'Name': ['a'], 'Score': [0], 'Strand': ['+']} {'Chromosome': ['chr1', 'chr1'], 'Start': [1, 6798349], 'End': [7130, 6808233], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['-', '-']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr6', 'chr18', 'chr20', 'chrX'], 'Start': [1120563, 8616082, 191345, 8616082, 6759631, 8616082, 6596020, 8616082, 8616082, 8616082], 'End': [1127246, 8622090, 193606, 8619988, 6769242, 8624236, 6604523, 8621032, 8624585, 8620609], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0, 0, 0, 0], 'Strand': ['+', '+', '+', '-', '-', '-', '+', '-', '+', '+']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr6', 'chr7', 'chr9', 'chr18', 'chr20'], 'Start': [7559161, 6534206, 3327597, 8676205, 7559161, 6936795, 2, 185195, 8707883, 9250607], 'End': [7559731, 6538746, 3331912, 8684152, 7560998, 6943085, 3920, 189974, 8717703, 9257730], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0, 0, 0, 0], 'Strand': ['+', '+', '+', '-', '-', '+', '-', '-', '-', '+']} {'Chromosome': ['chr5'], 'Start': [3166817], 'End': [3175166], 'Name': ['a'], 'Score': [0], 'Strand': ['+']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr4', 'chr5', 'chr7', 'chr12', 'chr14'], 'Start': [7062217, 7865023, 9869182, 8294298, 2706571, 1762288, 10000000, 2, 8460713, 1416479], 'End': [7072216, 7866521, 9879181, 8304297, 2716570, 1772287, 10009999, 10001, 8470712, 1426478], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0, 0, 0, 0], 'Strand': ['+', '+', '-', '-', '-', '-', '-', '+', '-', '-']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr10', 'chr10', 'chrM'], 'Start': [8526825, 10000000, 6492729, 5114179, 6339111, 7414076, 8461406], 'End': [8534194, 10001323, 6499996, 5117408, 6346871, 7423146, 8463166], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0], 'Strand': ['-', '-', '-', '-', '-', '-', '-']} {'Chromosome': ['chr1', 'chr1', 'chr4', 'chr7', 'chr12', 'chr14', 'chr19', 'chr20', 'chrM'], 'Start': [7834141, 9452333, 9452333, 9452333, 9469524, 9452333, 9452333, 9452333, 9452333], 'End': [7835485, 9454125, 9453393, 9458023, 9469967, 9460915, 9456210, 9458866, 9457099], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0, 0, 0], 'Strand': ['+', '-', '-', '-', '+', '-', '+', '-', '-']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr8', 'chr9', 'chr9', 'chr12', 'chr13'], 'Start': [1565228, 7559791, 5225616, 3562571, 2, 4619546, 3129881, 6901172, 7277705, 5969741], 'End': [1571299, 7564899, 5232536, 3565275, 709, 4628895, 3134868, 6907749, 7279183, 5970274], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0, 0, 0, 0], 'Strand': ['+', '+', '+', '+', '-', '-', '+', '-', '+', '-']} {'Chromosome': ['chr1', 'chr1', 'chr14'], 'Start': [4473518, 5508488, 2655161], 'End': [4479644, 5511367, 2656601], 'Name': ['a', 'a', 'a'], 'Score': [0, 0, 0], 'Strand': ['-', '-', '+']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr5', 'chr6', 'chr17', 'chr21'], 'Start': [2249791, 2249791, 3848815, 2249791, 389804, 2249791, 2249791, 2249791, 2249791, 2249791], 'End': [2249941, 2249941, 3848965, 2249941, 389954, 2249941, 2249941, 2249941, 2249941, 2249941], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0, 0, 0, 0], 'Strand': ['+', 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9143436], 'Name': ['a', 'a', 'a'], 'Score': [0, 0, 0], 'Strand': ['-', '+', '+']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr11', 'chr14', 'chr21'], 'Start': [8906980, 9083275, 318527, 9016573, 6123078, 9153429], 'End': [8908941, 9089270, 326810, 9017123, 6125341, 9158048], 'Name': ['a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0], 'Strand': ['+', '-', '-', '+', '+', '+']} {'Chromosome': ['chr1', 'chr1', 'chr5', 'chr6'], 'Start': [2369180, 2369180, 2369180, 2369180], 'End': [2373169, 2375982, 2379028, 2379078], 'Name': ['a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0], 'Strand': ['+', '-', '-', '+']} {'Chromosome': ['chr1', 'chr12', 'chr22', 'chrM', 'chrX'], 'Start': [2, 7983823, 4748797, 4426199, 3736462], 'End': [5041, 7984802, 4751202, 4436199, 3737040], 'Name': ['a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0], 'Strand': ['-', '-', '+', '+', '-']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr4', 'chr4', 'chr9', 'chr13', 'chr13', 'chr14', 'chr18'], 'Start': [1120099, 7042488, 6745545, 7407395, 5148967, 1120099, 5903323, 321202, 2, 2779686], 'End': [1123099, 7045407, 6754110, 7408758, 5151088, 1121498, 5906943, 324989, 9243, 2782686], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0, 0, 0, 0], 'Strand': ['+', '+', '-', '+', '-', '+', '+', '-', '+', '+']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr2', 'chr6', 'chr8'], 'Start': [6151865, 9023144, 2350959, 546719, 1003207, 892720, 2506801, 9414095], 'End': [6161768, 9026787, 2360958, 550985, 1005908, 892722, 2512579, 9416823], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0, 0], 'Strand': ['-', '-', '-', '-', '-', '-', '+', '-']} {'Chromosome': ['chr1', 'chr1'], 'Start': [3548881, 4251123], 'End': [3550586, 4261123], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['+', '+']} {'Chromosome': ['chr1', 'chr3', 'chr10', 'chr18'], 'Start': [7253928, 511182, 7253928, 9153976], 'End': [7255030, 515215, 7254827, 9158748], 'Name': ['a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0], 'Strand': ['+', '+', '-', '+']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr7', 'chr18', 'chrM'], 'Start': [3240256, 5067078, 5067078, 115656, 1, 5067078, 1965449], 'End': [3249473, 5072101, 5072101, 120679, 5024, 5072101, 1970472], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0], 'Strand': ['+', '+', '-', '-', '-', '-', '-']} {'Chromosome': ['chr1', 'chr2', 'chr2', 'chr2', 'chr10', 'chr11', 'chr17', 'chr17', 'chrX'], 'Start': [7399515, 2529269, 2529269, 2529269, 2529269, 5025534, 4167023, 2529269, 1], 'End': [7408519, 2537914, 2532728, 2532256, 2537914, 5034179, 4176830, 2537914, 8646], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0, 0, 0], 'Strand': ['+', '+', '+', '-', '+', '+', '+', '+', '+']} {'Chromosome': ['chr1', 'chr1', 'chr2', 'chr7', 'chr10', 'chr13', 'chr17', 'chr21'], 'Start': [9759403, 4201268, 2418014, 8323628, 8323628, 8323628, 4195947, 8369324], 'End': [9765283, 4207148, 2423894, 8329508, 8327257, 8329508, 4201827, 8375204], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0, 0], 'Strand': ['+', '-', '-', '+', '+', '+', '-', '-']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr9', 'chr22', 'chr22', 'chrX'], 'Start': [1, 7727625, 2011362, 4437133, 9717971, 1740543, 9004133, 1361230], 'End': [2, 7729836, 2017614, 4444686, 9722199, 1740544, 9011356, 1362040], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0, 0], 'Strand': ['+', '+', '+', '-', '+', '+', '-', '-']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1'], 'Start': [6854143, 261637, 261637, 1, 261637, 2479317], 'End': [6856261, 270186, 263722, 7291, 267927, 2485104], 'Name': ['a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0], 'Strand': ['+', '+', '+', '+', '-', '-']} {'Chromosome': ['chr1'], 'Start': [9999999], 'End': [10001302], 'Name': ['a'], 'Score': [0], 'Strand': ['+']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr7', 'chr7', 'chr15', 'chr21', 'chrM'], 'Start': [1289973, 5466886, 9362375, 9999999, 7457089, 8218708, 3581593, 6751558, 4352051, 7929919], 'End': [1297911, 5474824, 9370313, 10007937, 7465027, 8226793, 3589531, 6758587, 4361765, 7937857], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0, 0, 0, 0], 'Strand': ['+', '+', '+', '+', '-', '+', '-', '+', '+', '+']} {'Chromosome': ['chr1', 'chr1'], 'Start': [4518437, 4518437], 'End': [4520578, 4520578], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['+', '-']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr14', 'chr15', 'chr16', 'chrX'], 'Start': [3257935, 1, 3041537, 3284461, 6051178, 9585685, 290941, 4213419, 3284461], 'End': [3263443, 3812, 3048916, 3288699, 6060231, 9593362, 300940, 4221912, 3287523], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0, 0, 0], 'Strand': ['+', '+', '+', '-', '-', '+', '-', '-', '+']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr1'], 'Start': [579920, 171091, 146109, 6674062, 1422982], 'End': [587633, 172303, 151692, 6675774, 1423733], 'Name': ['a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0], 'Strand': ['+', '+', '-', '-', '-']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr18', 'chr21', 'chr21'], 'Start': [8902299, 8902299, 8902299, 3556503, 8902299, 8902299, 8902299, 8902299, 8902299, 8902299], 'End': [8909426, 8905706, 8902360, 3561100, 8902300, 8904638, 8902300, 8903177, 8904179, 8902986], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0, 0, 0, 0], 'Strand': ['+', '+', '-', '-', '-', '-', '-', '+', '+', '+']} {'Chromosome': ['chr1'], 'Start': [8759176], 'End': [8761679], 'Name': ['a'], 'Score': [0], 'Strand': ['-']} {'Chromosome': ['chr1', 'chr1', 'chr7', 'chr7', 'chr9'], 'Start': [4331880, 5063183, 9430874, 1411789, 6351873], 'End': [4334795, 5072615, 9437221, 1421221, 6352994], 'Name': ['a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0], 'Strand': ['+', '-', '+', '-', '-']} {'Chromosome': ['chr1', 'chr1'], 'Start': [8132201, 3832138], 'End': [8139719, 3839656], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['+', '-']} {'Chromosome': ['chr1', 'chr4', 'chr5', 'chr6', 'chr12', 'chr21'], 'Start': [6994514, 5204271, 3669512, 2207538, 8117302, 4477649], 'End': [7002507, 5211610, 3669608, 2209103, 8121234, 4483833], 'Name': ['a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0], 'Strand': ['-', '+', '+', '+', '+', '+']} {'Chromosome': ['chr1', 'chr10', 'chr21', 'chr21', 'chrX'], 'Start': [9509059, 8035404, 1366634, 2636397, 7545256], 'End': [9514127, 8044165, 1375495, 2645617, 7545730], 'Name': ['a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0], 'Strand': ['+', '+', '+', '-', '+']} {'Chromosome': ['chr1', 'chr10'], 'Start': [2704110, 2775307], 'End': [2708573, 2779391], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['+', '-']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr7', 'chr20'], 'Start': [3553504, 4505193, 3614104, 1846930, 660888, 76485, 1], 'End': [3559042, 4508935, 3616882, 1856078, 662818, 77599, 932], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0], 'Strand': ['+', '+', '-', '-', '-', '+', '+']} {'Chromosome': ['chr1', 'chr6'], 'Start': [7720640, 8195280], 'End': [7723226, 8199314], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['-', '+']} {'Chromosome': ['chr1', 'chr1', 'chr12', 'chr12', 'chr12', 'chr12', 'chrM', 'chrX'], 'Start': [4824967, 1053622, 7572539, 3138147, 6990006, 6815704, 3393031, 5634379], 'End': [4826261, 1053624, 7572541, 3138149, 6990008, 6815706, 3402314, 5634381], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0, 0], 'Strand': ['+', '+', '+', '+', '+', '-', '-', '-']} {'Chromosome': ['chr1'], 'Start': [9134748], 'End': [9136116], 'Name': ['a'], 'Score': [0], 'Strand': ['-']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr5', 'chrY'], 'Start': [8624026, 8624026, 5051547, 7725372, 4759257], 'End': [8631636, 8630720, 5056151, 7729619, 4761211], 'Name': ['a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0], 'Strand': ['+', '-', '-', '+', '-']} {'Chromosome': ['chr1'], 'Start': [513158], 'End': [514851], 'Name': ['a'], 'Score': [0], 'Strand': ['+']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr6', 'chr14', 'chr16', 'chr19'], 'Start': [7988374, 3157116, 8797975, 8965099, 8336820, 9981083, 4047082, 9981083, 1, 9813113], 'End': [7988925, 3164767, 8807066, 8974324, 8344839, 9982784, 4056290, 9984597, 756, 9819425], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0, 0, 0, 0], 'Strand': ['+', '+', '-', '-', '-', '-', '+', '-', '-', '+']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr4', 'chr10'], 'Start': [4680932, 4680932, 4680932, 4680932, 4680932, 4680932], 'End': [4689254, 4690360, 4685950, 4686621, 4681942, 4688500], 'Name': ['a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0], 'Strand': ['+', '+', '-', '-', '+', '-']} {'Chromosome': ['chr1', 'chr11', 'chrM'], 'Start': [3602632, 8334593, 9030792], 'End': [3607462, 8339851, 9033666], 'Name': ['a', 'a', 'a'], 'Score': [0, 0, 0], 'Strand': ['-', '-', '-']} {'Chromosome': ['chr7'], 'Start': [7638603], 'End': [7643548], 'Name': ['a'], 'Score': [0], 'Strand': ['-']} {'Chromosome': ['chr1', 'chr1', 'chr22'], 'Start': [1193482, 1920852, 1601232], 'End': [1199704, 1927074, 1607454], 'Name': ['a', 'a', 'a'], 'Score': [0, 0, 0], 'Strand': ['+', '-', '+']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr6', 'chr8', 'chr17', 'chr20', 'chrY'], 'Start': [8712222, 8712222, 8712222, 8712222, 8712222, 8712222, 8712222, 8712222, 8712222, 8712222], 'End': [8717441, 8712223, 8712799, 8717015, 8717754, 8721598, 8712518, 8716158, 8715663, 8712518], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0, 0, 0, 0], 'Strand': ['+', '+', '+', '+', '+', '+', '-', '+', '-', '+']} {'Chromosome': ['chr4', 'chrM', 'chrY'], 'Start': [2697835, 423529, 8146244], 'End': [2707224, 427851, 8153483], 'Name': ['a', 'a', 'a'], 'Score': [0, 0, 0], 'Strand': ['-', '-', '-']} {'Chromosome': ['chr1'], 'Start': [9999999], 'End': [10007254], 'Name': ['a'], 'Score': [0], 'Strand': ['-']} {'Chromosome': ['chr1', 'chr1', 'chr18', 'chr19', 'chrY'], 'Start': [8065916, 5499633, 3807043, 5957161, 8658901], 'End': [8068437, 5508841, 3816515, 5962383, 8662911], 'Name': ['a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0], 'Strand': ['+', '+', '+', '-', '-']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr12', 'chr12', 'chr17', 'chr18'], 'Start': [9974992, 4124660, 5323592, 6599078, 1382271, 3279222, 10000000, 10000000, 5404869, 6745374], 'End': [9977976, 4133454, 5326747, 6604678, 1382272, 3287319, 10002506, 10007571, 5410126, 6746609], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0, 0, 0, 0], 'Strand': ['+', '+', '-', '-', '-', '-', '+', '+', '+', '+']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr6'], 'Start': [4677395, 3064728, 9834507, 4148225, 5940047, 3915419, 3887620], 'End': [4686264, 3070496, 9835913, 4151857, 5941424, 3921561, 3892600], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0], 'Strand': ['+', '+', '-', '-', '-', '-', '-']} {'Chromosome': ['chr1'], 'Start': [772584], 'End': [777252], 'Name': ['a'], 'Score': [0], 'Strand': ['-']} {'Chromosome': ['chr1', 'chr1', 'chr3', 'chr5'], 'Start': [7406081, 5970399, 296257, 3022464], 'End': [7409471, 5978733, 302714, 3022995], 'Name': ['a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0], 'Strand': ['-', '-', '-', '-']} {'Chromosome': ['chr5'], 'Start': [5226157], 'End': [5231854], 'Name': ['a'], 'Score': [0], 'Strand': ['+']} {'Chromosome': ['chr1'], 'Start': [3601473], 'End': [3606983], 'Name': ['a'], 'Score': [0], 'Strand': ['+']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr6', 'chr13', 'chr21'], 'Start': [8411655, 1602971, 7246728, 5323963, 8228789, 9862077, 6178003, 3675736, 4476709, 4528016], 'End': [8415411, 1610527, 7248370, 5332803, 8230315, 9871914, 6186965, 3685736, 4483088, 4537450], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0, 0, 0, 0], 'Strand': ['+', '+', '+', '-', '-', '-', '-', '-', '+', '-']} {'Chromosome': ['chr9', 'chr9', 'chr9', 'chr9', 'chr9', 'chr21'], 'Start': [6188334, 7866624, 9079304, 6318370, 3292983, 9083582], 'End': [6195065, 7867849, 9081383, 6326837, 3295383, 9087763], 'Name': ['a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0], 'Strand': ['+', '+', '+', '+', '+', '+']} {'Chromosome': ['chr17'], 'Start': [2], 'End': [62], 'Name': ['a'], 'Score': [0], 'Strand': ['-']} {'Chromosome': ['chr18'], 'Start': [9858917], 'End': [9861632], 'Name': ['a'], 'Score': [0], 'Strand': ['+']} {'Chromosome': ['chr1', 'chr1', 'chr7', 'chr14'], 'Start': [512402, 7579610, 6969157, 6565073], 'End': [513872, 7579646, 6972030, 6565109], 'Name': ['a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0], 'Strand': ['-', '-', '-', '-']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr4', 'chr16', 'chrM', 'chrM', 'chrY'], 'Start': [1154053, 354597, 1154053, 8621691, 4800323, 1154053, 9401943, 3790735], 'End': [1161436, 363951, 1161436, 8629074, 4807706, 1161436, 9409326, 3799952], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0, 0], 'Strand': ['+', '-', '-', '-', '+', '+', '-', '+']} {'Chromosome': ['chr20'], 'Start': [2523141], 'End': [2530222], 'Name': ['a'], 'Score': [0], 'Strand': ['+']} {'Chromosome': ['chr22', 'chrM'], 'Start': [1779352, 5611751], 'End': [1781173, 5620452], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['+', '+']} {'Chromosome': ['chr1', 'chr1', 'chr16'], 'Start': [834264, 9704664, 6449852], 'End': [837825, 9712133, 6452610], 'Name': ['a', 'a', 'a'], 'Score': [0, 0, 0], 'Strand': ['-', '-', '+']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr2', 'chr5', 'chr6', 'chr17', 'chr19'], 'Start': [6259898, 4767259, 3477552, 6203545, 10000000, 337561, 6491071, 7339493, 7096430, 5037632], 'End': [6264265, 4775194, 3481974, 6210660, 10008024, 338748, 6492258, 7340680, 7097944, 5041702], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0, 0, 0, 0], 'Strand': ['+', '+', '-', '-', '-', '-', '+', '+', '+', '-']} {'Chromosome': ['chr1'], 'Start': [1], 'End': [2], 'Name': ['a'], 'Score': [0], 'Strand': ['+']} =============================== warnings summary =============================== tests/conftest.py:83 /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/conftest.py:83: SyntaxWarning: invalid escape sequence '\s' sep="\s+", pyranges/__init__.py:18: 12 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/__init__.py:18: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html import pkg_resources tests/test_binary.py:118: 11 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py:118: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_binary.py:139: 11 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py:139: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_binary.py:160: 11 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py:160: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_binary.py:187: 11 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py:187: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_binary.py:212: 11 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py:212: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_binary.py:291: 11 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py:291: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_binary.py:329: 11 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py:329: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_binary.py:368: 11 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py:368: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_binary.py:392: 11 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py:392: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_binary.py:426: 11 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py:426: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_binary.py:516: 11 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py:516: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_binary.py:579: 11 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py:579: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) pyranges/methods/init.py:60: 55 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_change_chromosome_custom.py: 2 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_concat.py: 8 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_count_overlaps.py: 1 warning .pybuild/cpython3_3.12_pyranges/build/tests/data/test_data.py: 9 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py: 56343 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py: 442635 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py: 4 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_getset_attr.py: 3 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_io.py: 4 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_pickle.py: 1 warning .pybuild/cpython3_3.12_pyranges/build/tests/test_stranded.py: 6 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_unary.py: 20820 warnings .pybuild/cpython3_3.12_pyranges/build/tests/windows/test_windows.py: 2 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/init.py:60: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning. return {k: v for k, v in df.groupby(grpby_key)} pyranges/methods/init.py:189: 44 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_change_chromosome_custom.py: 1 warning .pybuild/cpython3_3.12_pyranges/build/tests/test_concat.py: 7 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py: 5289 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py: 708 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_stranded.py: 2 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_unary.py: 4900 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/init.py:189: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning. empty_removed = df.groupby("Chromosome") tests/test_do_not_error.py:46: 11 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py:46: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_unary.py:35: 11 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_unary.py:35: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_unary.py:100: 11 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_unary.py:100: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_unary.py:163: 11 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_unary.py:163: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_unary.py:205: 11 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_unary.py:205: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_unary.py:234: 11 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_unary.py:234: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_unary.py:272: 11 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_unary.py:272: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_unary.py:287: 11 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_unary.py:287: HypothesisDeprecationWarning: The return_value health check is deprecated, because this is always an error. @settings( tests/test_unary.py:315: 11 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_unary.py:315: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) .pybuild/cpython3_3.12_pyranges/build/tests/test_concat.py::test_concat_stranded_unstranded /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:47: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['+', '+', '-', NaN, NaN] Categories (3, object): ['+', '-', '.']' has dtype incompatible with category, please explicitly cast to a compatible dtype first. v.loc[:, "Strand"] = type_v.cat.add_categories(["."]) .pybuild/cpython3_3.12_pyranges/build/tests/test_concat.py: 1 warning .pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py: 3287 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py: 1 warning .pybuild/cpython3_3.12_pyranges/build/tests/test_stranded.py: 2 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_unary.py: 4784 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/init.py:187: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning. empty_removed = df.groupby(["Chromosome", "Strand"]) .pybuild/cpython3_3.12_pyranges/build/tests/test_concat.py::test_concat_unstranded_stranded /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:47: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[NaN, NaN, NaN, '+', '-'] Categories (3, object): ['+', '-', '.']' has dtype incompatible with category, please explicitly cast to a compatible dtype first. v.loc[:, "Strand"] = type_v.cat.add_categories(["."]) .pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py: 7745 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py: 72591 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_unary.py: 6582 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/tostring2.py:31: FutureWarning: The behavior of DataFrame concatenation with empty or all-NA entries is deprecated. In a future version, this will no longer exclude empty or all-NA columns when determining the result dtypes. To retain the old behavior, exclude the relevant entries before the concat operation. df = pd.concat([plus, minus]) .pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py: 2604 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:3779: FutureWarning: The behavior of Series.replace (and DataFrame.replace) with CategoricalDtype is deprecated. In a future version, replace will only be used for cases that preserve the categories. To change the categories, use ser.cat.rename_categories instead. other.Strand = other.Strand.replace({"+": "-", "-": "+"}) .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1217804. 1221351. 1223357. 1223968. 1227319. 1228946. 1232031.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_unary.py: 2000 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_unary.py:178: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning. for _, gdf in natsorted(df.groupby(groupby)): -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html =========================== short test summary info ============================ FAILED tests/test_binary.py::test_k_nearest[upstream-False-same-last] - Value... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain55-method_chain55] FAILED tests/test_binary.py::test_k_nearest[upstream-False-False-last] - Exce... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain19-method_chain19] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain43-method_chain43] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain7-method_chain7] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain0-method_chain0] FAILED tests/test_binary.py::test_jaccard[same] - Exception: Starts/Ends not ... FAILED tests/test_binary.py::test_nearest[upstream-True-same] - ExceptionGrou... FAILED tests/test_binary.py::test_set_intersect[False] - Exception: Starts/En... FAILED tests/test_binary.py::test_coverage[same] - Exception: Starts/Ends not... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain31-method_chain31] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain56-method_chain56] FAILED tests/test_binary.py::test_k_nearest[upstream-True-opposite-last] - Ex... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain8-method_chain8] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain33-method_chain33] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain1-method_chain1] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain21-method_chain21] FAILED tests/test_binary.py::test_k_nearest[upstream-True-same-last] - Except... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain45-method_chain45] FAILED tests/test_binary.py::test_set_intersect[same] - Exception: Starts/End... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain57-method_chain57] FAILED tests/test_binary.py::test_nearest[upstream-True-opposite] - Exception... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain9-method_chain9] FAILED tests/test_binary.py::test_coverage[opposite] - Exception: Starts/Ends... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain2-method_chain2] FAILED tests/test_binary.py::test_k_nearest[upstream-True-False-last] - Excep... FAILED tests/test_binary.py::test_nearest[upstream-False-False] - ExceptionGr... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain58-method_chain58] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain10-method_chain10] FAILED tests/test_binary.py::test_k_nearest[None-False-opposite-last] - Value... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain47-method_chain47] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain35-method_chain35] FAILED tests/test_binary.py::test_k_nearest[None-False-same-last] - ValueErro... FAILED tests/test_binary.py::test_nearest[upstream-False-same] - ExceptionGro... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain3-method_chain3] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain22-method_chain22] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain59-method_chain59] FAILED tests/test_binary.py::test_k_nearest[None-False-False-last] - ValueErr... FAILED tests/test_binary.py::test_subtraction[same] - Exception: Starts/Ends ... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain11-method_chain11] FAILED tests/test_binary.py::test_set_union[False] - Exception: Starts/Ends n... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain60-method_chain60] FAILED tests/test_binary.py::test_nearest[upstream-False-opposite] - Exceptio... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain4-method_chain4] FAILED tests/test_binary.py::test_k_nearest[None-True-opposite-last] - ValueE... FAILED tests/test_binary.py::test_k_nearest[None-True-same-last] - ValueError... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain49-method_chain49] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain36-method_chain36] FAILED tests/test_binary.py::test_k_nearest[None-True-False-last] - ValueErro... FAILED tests/test_binary.py::test_k_nearest_1_vs_nearest - ValueError: Buffer... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain12-method_chain12] FAILED tests/test_binary.py::test_nearest[downstream-True-False] - ExceptionG... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain23-method_chain23] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain61-method_chain61] FAILED tests/test_binary.py::test_subtraction[opposite] - Exception: Starts/E... FAILED tests/test_binary.py::test_set_union[same] - Exception: Starts/Ends no... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain37-method_chain37] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain5-method_chain5] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain13-method_chain13] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain77-method_chain77] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain50-method_chain50] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain62-method_chain62] FAILED tests/test_binary.py::test_k_nearest[downstream-False-opposite-last] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain24-method_chain24] FAILED tests/test_binary.py::test_nearest[downstream-True-same] - ExceptionGr... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain51-method_chain51] FAILED tests/test_binary.py::test_subtraction[False] - Exception: Starts/Ends... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain6-method_chain6] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain78-method_chain78] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain14-method_chain14] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain63-method_chain63] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain38-method_chain38] FAILED tests/test_binary.py::test_k_nearest[downstream-False-same-last] - Exc... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain52-method_chain52] FAILED tests/test_binary.py::test_nearest[None-True-False] - ExceptionGroup: ... FAILED tests/test_binary.py::test_nearest[downstream-True-opposite] - Excepti... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain25-method_chain25] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain68-method_chain68] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain64-method_chain64] FAILED tests/test_binary.py::test_k_nearest[downstream-False-False-last] - Ex... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain15-method_chain15] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain39-method_chain39] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain53-method_chain53] FAILED tests/test_binary.py::test_nearest[downstream-False-False] - Exception... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain80-method_chain80] FAILED tests/test_binary.py::test_nearest[None-True-same] - ExceptionGroup: H... FAILED tests/test_binary.py::test_k_nearest[downstream-True-opposite-last] - ... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain26-method_chain26] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain40-method_chain40] FAILED tests/test_binary.py::test_k_nearest[downstream-True-same-last] - Valu... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain17-method_chain17] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain70-method_chain70] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain54-method_chain54] FAILED tests/test_binary.py::test_nearest[downstream-False-same] - ExceptionG... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain66-method_chain66] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain82-method_chain82] FAILED tests/test_binary.py::test_nearest[None-True-opposite] - ExceptionGrou... FAILED tests/test_binary.py::test_k_nearest[downstream-True-False-last] - Exc... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain27-method_chain27] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain41-method_chain41] FAILED tests/test_binary.py::test_nearest[None-False-False] - ValueError: Buf... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain71-method_chain71] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain108-method_chain108] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain123-method_chain123] FAILED tests/test_binary.py::test_nearest[downstream-False-opposite] - Except... FAILED tests/test_binary.py::test_nearest[None-False-same] - ValueError: Buff... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain94-method_chain94] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain84-method_chain84] FAILED tests/test_binary.py::test_k_nearest[upstream-False-opposite-last] - E... FAILED tests/test_binary.py::test_nearest[None-False-opposite] - ValueError: ... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain28-method_chain28] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain109-method_chain109] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain42-method_chain42] FAILED tests/test_binary.py::test_jaccard[False] - Exception: Starts/Ends not... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain72-method_chain72] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain124-method_chain124] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain96-method_chain96] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain85-method_chain85] FAILED tests/test_binary.py::test_nearest[upstream-True-False] - ExceptionGro... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain137-method_chain137] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain150-method_chain150] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain29-method_chain29] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain110-method_chain110] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain73-method_chain73] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain151-method_chain151] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain138-method_chain138] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain125-method_chain125] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain86-method_chain86] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain164-method_chain164] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain175-method_chain175] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain98-method_chain98] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain111-method_chain111] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain126-method_chain126] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain187-method_chain187] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain176-method_chain176] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain166-method_chain166] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain74-method_chain74] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain152-method_chain152] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain139-method_chain139] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain112-method_chain112] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain87-method_chain87] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain99-method_chain99] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain127-method_chain127] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain188-method_chain188] FAILED tests/test_binary.py::test_coverage[False] - Exception: Starts/Ends no... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain153-method_chain153] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain100-method_chain100] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain140-method_chain140] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain113-method_chain113] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain178-method_chain178] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain88-method_chain88] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain75-method_chain75] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain198-method_chain198] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain168-method_chain168] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain189-method_chain189] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain101-method_chain101] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain129-method_chain129] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain154-method_chain154] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain141-method_chain141] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain199-method_chain199] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain89-method_chain89] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain180-method_chain180] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain102-method_chain102] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain190-method_chain190] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain131-method_chain131] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain76-method_chain76] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain115-method_chain115] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain200-method_chain200] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain169-method_chain169] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain155-method_chain155] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain90-method_chain90] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain143-method_chain143] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain209-method_chain209] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain156-method_chain156] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain103-method_chain103] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain182-method_chain182] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain117-method_chain117] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain201-method_chain201] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain133-method_chain133] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain192-method_chain192] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain170-method_chain170] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain157-method_chain157] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain104-method_chain104] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain91-method_chain91] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain210-method_chain210] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain145-method_chain145] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain202-method_chain202] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain183-method_chain183] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain158-method_chain158] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain211-method_chain211] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain194-method_chain194] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain134-method_chain134] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain105-method_chain105] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain119-method_chain119] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain184-method_chain184] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain92-method_chain92] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain171-method_chain171] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain203-method_chain203] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain147-method_chain147] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain159-method_chain159] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain135-method_chain135] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain196-method_chain196] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain106-method_chain106] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain213-method_chain213] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain160-method_chain160] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain204-method_chain204] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain185-method_chain185] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain148-method_chain148] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain120-method_chain120] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain219-method_chain219] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain172-method_chain172] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain107-method_chain107] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain197-method_chain197] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain136-method_chain136] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain149-method_chain149] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain205-method_chain205] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain161-method_chain161] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain186-method_chain186] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain215-method_chain215] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain247-method_chain247] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain238-method_chain238] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain206-method_chain206] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain121-method_chain121] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain220-method_chain220] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain162-method_chain162] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain229-method_chain229] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain264-method_chain264] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain173-method_chain173] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain248-method_chain248] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain255-method_chain255] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain239-method_chain239] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain207-method_chain207] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain256-method_chain256] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain249-method_chain249] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain217-method_chain217] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain174-method_chain174] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain231-method_chain231] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain221-method_chain221] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain122-method_chain122] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain271-method_chain271] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain250-method_chain250] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain266-method_chain266] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain208-method_chain208] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain257-method_chain257] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain285-method_chain285] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain241-method_chain241] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain278-method_chain278] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain251-method_chain251] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain218-method_chain218] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain292-method_chain292] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain232-method_chain232] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain258-method_chain258] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain222-method_chain222] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain272-method_chain272] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain298-method_chain298] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain243-method_chain243] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain267-method_chain267] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain286-method_chain286] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain233-method_chain233] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain252-method_chain252] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain259-method_chain259] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain280-method_chain280] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain294-method_chain294] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain273-method_chain273] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain299-method_chain299] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain223-method_chain223] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain245-method_chain245] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain260-method_chain260] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain287-method_chain287] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain253-method_chain253] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain268-method_chain268] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain274-method_chain274] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain295-method_chain295] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain281-method_chain281] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain234-method_chain234] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain300-method_chain300] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain254-method_chain254] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain296-method_chain296] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain224-method_chain224] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain246-method_chain246] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain288-method_chain288] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain282-method_chain282] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain235-method_chain235] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain297-method_chain297] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain301-method_chain301] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain269-method_chain269] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain225-method_chain225] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain262-method_chain262] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain304-method_chain304] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain276-method_chain276] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain305-method_chain305] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain236-method_chain236] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain311-method_chain311] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain302-method_chain302] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain331-method_chain331] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain321-method_chain321] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain290-method_chain290] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain283-method_chain283] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain270-method_chain270] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain303-method_chain303] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain316-method_chain316] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain227-method_chain227] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain237-method_chain237] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain306-method_chain306] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain313-method_chain313] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain322-method_chain322] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain284-method_chain284] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain352-method_chain352] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain327-method_chain327] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain307-method_chain307] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain341-method_chain341] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain332-method_chain332] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain344-method_chain344] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain317-method_chain317] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain336-method_chain336] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain353-method_chain353] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain323-method_chain323] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain348-method_chain348] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain345-method_chain345] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain308-method_chain308] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain343-method_chain343] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain315-method_chain315] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain333-method_chain333] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain337-method_chain337] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain354-method_chain354] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain318-method_chain318] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain346-method_chain346] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain329-method_chain329] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain349-method_chain349] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain334-method_chain334] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain356-method_chain356] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain309-method_chain309] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain347-method_chain347] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain325-method_chain325] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain355-method_chain355] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain350-method_chain350] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain335-method_chain335] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain360-method_chain360] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain319-method_chain319] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain357-method_chain357] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain330-method_chain330] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain339-method_chain339] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain376-method_chain376] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain364-method_chain364] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain362-method_chain362] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain351-method_chain351] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain358-method_chain358] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain366-method_chain366] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain372-method_chain372] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain369-method_chain369] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain390-method_chain390] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain378-method_chain378] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain381-method_chain381] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain320-method_chain320] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain383-method_chain383] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain388-method_chain388] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain397-method_chain397] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain382-method_chain382] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain365-method_chain365] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain385-method_chain385] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain370-method_chain370] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain392-method_chain392] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain367-method_chain367] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain379-method_chain379] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain374-method_chain374] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain384-method_chain384] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain402-method_chain402] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain398-method_chain398] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain395-method_chain395] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain401-method_chain401] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain403-method_chain403] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain386-method_chain386] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain393-method_chain393] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain371-method_chain371] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain405-method_chain405] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain380-method_chain380] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain396-method_chain396] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain399-method_chain399] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain368-method_chain368] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain404-method_chain404] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain411-method_chain411] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain394-method_chain394] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain407-method_chain407] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain406-method_chain406] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain421-method_chain421] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain400-method_chain400] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain415-method_chain415] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain414-method_chain414] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain428-method_chain428] FAILED tests/test_genomicfeatures.py::test_introns_single - ValueError: Buffe... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain427-method_chain427] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain413-method_chain413] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain425-method_chain425] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain420-method_chain420] FAILED tests/test_unary.py::test_merge[True] - Exception: Starts/Ends not int... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain416-method_chain416] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain419-method_chain419] FAILED tests/test_unary.py::test_merge[False] - Exception: Starts/Ends not in... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain439-method_chain439] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain418-method_chain418] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain429-method_chain429] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain417-method_chain417] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain434-method_chain434] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain433-method_chain433] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain432-method_chain432] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain431-method_chain431] FAILED tests/windows/test_windows.py::test_windows - ValueError: Buffer dtype... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain430-method_chain430] FAILED tests/test_unary.py::test_cluster[True] - Exception: Starts/Ends not i... FAILED tests/windows/test_windows.py::test_windows2 - ValueError: Buffer dtyp... FAILED tests/test_unary.py::test_windows - Exception: Starts/Ends not int64 o... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain435-method_chain435] FAILED tests/test_unary.py::test_cluster[False] - Exception: Starts/Ends not ... FAILED tests/test_unary.py::test_summary - Exception: Starts/Ends not int64 o... ======== 415 failed, 116 passed, 630688 warnings in 9773.00s (2:42:52) ========= E: pybuild pybuild:389: test: plugin distutils failed with: exit code=1: cd /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build; python3.12 -m pytest -v -n 11 dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.12 returned exit code 13 make: *** [debian/rules:22: binary] Error 25 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 I: copying local configuration E: Failed autobuilding of package I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/9137 and its subdirectories